Inhibitors of cyclin dependent kinase 7 (cdk7)

ABSTRACT

The present invention provides, inter alia, compounds having the structures of formulas described herein; pharmaceutically acceptable salts, solvates, hydrates, tautomers, and isotopic forms thereof; and compositions (e.g., pharmaceutical compositions and kits) containing one or more of the foregoing. Also provided are methods of administering and uses involving the compounds and/or pharmaceutical compositions for treating or preventing disease. The disease can be a proliferative disease, such as a cancer (e.g., a blood cancer (e.g., a leukemia or lymphoma), a brain cancer, a breast cancer, melanoma, multiple myeloma, or an ovarian cancer) a benign neoplasm, pathologic angiogenesis, or a fibrotic disease. While no aspect of the invention is limited by the biological events that may transpire, administering a compound or other composition described herein may selectively inhibit the aberrant expression or activity of cyclin-dependent kinase 7 (CDK7) and, thereby, induce cellular apoptosis and/or inhibit the transcription of disease-related genes in the patient (or in a biological sample).

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of the filing date of U.S. Provisional Application No. 62/617,884, filed Jan. 16, 2018, the entire content of which is hereby incorporated by reference herein.

BACKGROUND OF THE INVENTION

Kinases that are members of the cyclin-dependent kinase (CDK) family play critical roles in cellular proliferation. Among the mammalian CDKs, CDK7 has uniquely consolidated kinase activities that help regulate both the cell cycle and gene transcription. In the cytosol, CDK7 exists within a heterotrimeric complex and is thought to function as a CDK1/2-activating kinase (CAK); phosphorylation of conserved residues in CDK1/2 by CDK7 is required for full catalytic activity and cell cycle progression. In the nucleus, CDK7 forms the kinase core of the RNA polymerase (RNAP) II general transcription factor complex and phosphorylates its C-terminal domain (CTD), a requisite step in initiating gene transcription. By both activating CDK1/2 and phosphorylating the CTD of RNAP II, CDK7 supports critical facets of cellular proliferation, cell cycling, and gene transcription.

Although some progress has been made, it is difficult to develop selective inhibitors of CDK7 because its sequence and structure are similar to the sequences and structures of other CDKs. Thus, there is still an unmet need for selective CKD7 inhibitors.

SUMMARY OF THE INVENTION

Described herein are selective CDK7 inhibitors (compounds) of Formula (I) and pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, and isotopic forms thereof. These compounds preferably demonstrate greater specificity for CDK7 than for one or more of CDK2, CDK9, and CDK12 (e.g., at least 10-, 100-, or 1,000-fold greater specificity) when assessed in an enzymatic assay that measures the IC₅₀ of the compound. Also described are compositions containing a compound described herein (e.g., a pharmaceutical composition or kit) and methods of using the compounds (or salts, solvates (e.g., hydrates), tautomers, and isotopic forms thereof), pharmaceutical compositions, or kits to treat or prevent a disease associated with aberrant CDK7 expression (e.g., overexpression or misexpression) or activity (e.g., overactivity). The disease can be a proliferative disease (e.g., a cancer such as a blood cancer (e.g., leukemia) breast cancer, melanoma, multiple myeloma, ovarian cancer (or any other cancer described further below), a benign neoplasm, or a condition characterized by pathologic angiogenesis, or a fibrotic disease). The fibrotic disease can be NASH (non-alcoholic steatohepatitis) or NAFLD (non-alcoholic fatty liver disease), which can progress to cirrhosis of the liver and eventual liver failure; any other disease or chronic damage to the liver that results in fibrosis (e.g., alcoholism or hepatitis); scleroderma, which can progress to systemic scleroderma (also known as systemic sclerosis (SSc)); any other disease characterized by cutaneous fibrosis or resulting in pulmonary fibrosis (e.g., cystic fibrosis, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus (SLE), or idiopathic pulmonary fibrosis); kidney fibrosis (e.g., as occurs in connection with chronic kidney disease such as Alport Syndrome, glomerulonephritis, polycystic kidney disease, and reflux nephropathy); and cardiac (e.g., endomyocardial) fibrosis, which is a common phenomenon in heart or cardiovascular diseases such as ischemic heart disease, atherosclerosis, arteriosclerosis, and inherited cardiomyopathies, as well as in Behcet's disease, diabetes, and ageing. The disease can also be an infectious disease (e.g., a viral infection caused by an influenza virus, human immunodeficiency virus (HIV), herpes virus, or human papilloma virus (HPV)) or a disease caused by or associated with expanded repeats of simple nucleotide tracts including, but not limited to, Huntington's Disease (HD), myotonic dystrophy (e.g., DM1 and DM2), and some forms of amyotrophic lateral sclerosis (ALS). Diseases caused by or associated with an expanded repeat are also known in the art as trinucleotide repeat disorders, trinucleotide repeat expansion disorders, triplet repeat expansion disorders, and codon reiteration disorders. In these genetic diseases, trinucleotide repeats in certain genes or introns exceed the stable threshold observed in healthy patients.

In one aspect, the present invention provides compounds of formula (I)

and pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, and isotopically labeled derivatives thereof, wherein Ring A, Ring B, X, Y, R¹ and subvariables thereof are as defined herein. For ease of reading, we may not refer to both a compound of the invention and a pharmaceutically acceptable salt thereof when describing each and every composition, method, and use within the scope of the invention. It is to be understood that where a compound of the invention can be used, a pharmaceutically acceptable salt thereof may also be useful, and making that determination is well within the ability of one of ordinary skill in the art.

While pharmaceutical compositions within the scope of the invention are described further below, we note here that they can contain a compound of Formula (I) (or a pharmaceutically acceptable salt, solvate (e.g., hydrate), tautomer, or isotopic form thereof) and a pharmaceutically acceptable excipient. The active ingredient (e.g., a compound of Formula (I)), regardless of its precise chemical form (e.g., isomeric or isotopic forms), can be present in a therapeutically or prophylactically effective amount, and the pharmaceutical compositions described herein can be packaged in unit dosages, fractions thereof or multiples thereof.

In addition to administering a composition described herein to a patient who has been diagnosed as having a disease described herein, the compositions of the invention can be used ex vivo to alter CDK7 expression or activity in a biological sample (e.g., a cultured cell line or a blood or tissue sample obtained from a patient). In any circumstance in which a compound or composition described herein is administered to a patient, the patient may have been diagnosed with a disease that is associated with aberrant expression or activity of CDK7, and any of the methods of treatment or uses described herein can include a step of determining whether CDK7 expression or activity is aberrant in a biological sample obtained from the patient. This information may also be obtained indirectly. Thus, the methods of treatment and uses described herein can include a step of administering/using a compound or composition described herein, where, prior to the administration/use, a biological sample obtained from the patient has been determined to exhibit aberrant (e.g., elevated) CDK7 expression or activity.

The kits can include a container with a compound of Formula (I) or a pharmaceutically acceptable salt, solvate (e.g., hydrate), tautomer, or isotopic form thereof, or a pharmaceutical composition thereof. In certain embodiments, the kits described herein further include instructions (in written or other form) for administering a compound described herein (e.g., a compound of Formula (I) or a pharmaceutically acceptable salt, solvate (e.g., hydrate), tautomer, or isotopic form thereof, or the pharmaceutical composition thereof. Paraphernalia (e.g., a syringe, needles, tubing, gloves, bandages, tape, local anestheics, etc. . . . ) may also be included.

The following definitions apply to the compositions and methods described herein unless the context clearly indicates otherwise. It will be evident to one of ordinary skill in the art that the definitions apply to grammatical variants of these terms, some of which are particularly mentioned below (e.g., “administration” and “administering”). The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed. Additionally, general principles of organic chemistry that may facilitate the production of the compounds described herein can be found in “Organic Chemistry,” Thomas Sorrell, University Science Books, Sausalito, 1999; “March's Advanced Organic Chemistry,” 5^(th) Ed., Ed. Smith and March, John Wiley & Sons, New York, 2001; Larock, “Comprehensive Organic Transformations,” VCH Publishers, Inc., New York, 1989; and Carruthers, “Some Modern Methods of Organic Synthesis,” 3^(rd) Edition, Cambridge University Press, Cambridge, 1987.

The term “about,” when used in reference to a value, signifies any value or range of values that is plus-or-minus 10% of the stated value (e.g., within plus-or-minus 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% or 10% of the stated value). For example, a dose of about 10 mg means any dose as low as 10% less than 10 mg (9 mg), any dose as high as 10% more than 10 mg (11 mg), and any dose or dosage range therebetween (e.g., 9-11 mg; 9.1-10.9 mg; 9.2-10.8 mg; and so on). In case of any doubt, the stated value is included; about 10 mg includes 10 mg. Where a stated value cannot be exceeded (e.g., 100%), “about” means a value or range of values that is up to and including 10% less than the stated value (e.g., a purity of about 100% means 90%-100% pure (e.g., 95%-100% pure, 96%-100% pure, 97%-100% pure etc. . . . )).

The term “administration” and variants thereof, such as “administering,” refer to the application of a compound described herein, a form thereof (e.g., a pharmaceutically acceptable salt or solvate) or a composition containing any such compounds or forms (e.g., a pharmaceutical composition) to a patient (e.g., a human patient) or system (e.g., a cell- or tissue-containing system maintained ex vivo (e.g., any cell, tissue, or organ culture, which may be maintained by conventional or new techniques). One of ordinary skill in the art will know a variety of routes that may, in appropriate circumstances, be utilized for administration to a patient or system. For example, the route of administration to a patient may be oral (i.e., by swallowing a pharmaceutical composition) or parenteral (a term encompassing any route of administration that is not oral; e.g., intra-arterial or intravenous, intra-articular, intracranial, intralesional, intramuscular, intraperitoneal, or intrathecal). Preferably, the compositions are administered orally, subcutaneously, intralesionally, intraperitoneally or intravenously. Any pharmaceutical composition described herein can be sterile and/or in an orally available or injectable form made using techniques and excipients known in the art (including those described further herein).

Further, the route of administration to a patient can be bronchial (e.g., by bronchial instillation), by mouth (i.e., oral), dermal (which may be or comprise topical application to the dermis or intradermal, interdermal, or transdermal administration), intragastric or enteral (i.e., directly to the stomach or intestine, respectively), intramedullary, intramuscular, intranasal, intraperitoneal, intrathecal, intravenous (or intra-arterial), intraventricular, by application to or injection into a specific organ (e.g., intrahepatic), mucosal (e.g., buccal, rectal, sublingual, or vaginal), subcutaneous, tracheal (e.g., by intratracheal instillation), or ocular (e.g., topical, subconjunctival, or intravitreal). Administration can involve continuous dosing (e.g., by oral administration or perfusion) for a selected time (e.g., over or every 1-3 hours; 3-6 hours; over a period of 12 hours; over a period of 24 hours; etc. . . . ), intermittent dosing (e.g., a plurality of doses separated in time), and/or periodic dosing (e.g., doses separated by a common period of time (e.g., every so many hours, daily, weekly, twice per week, etc.)).

The term “angiogenesis” refers to the formation and growth of new blood vessels. Normal angiogenesis occurs in healthy patients during development and in the context of wound healing. However, patients suffering from many different diseases, including cancer, diabetes (particularly the progression to blindness associated therewith), age-related macular degeneration, rheumatoid arthritis, and psoriasis, experience excessive and detrimental angiogenesis. Angiogenesis is detrimental when it produces blood vessels that support diseased cells (e.g., tumor cells), destroy normal tissues (e.g., tissue within the eye), or facilitates tumor metastases. We may refer to such unwanted angiogenesis as “pathologic angiogenesis.”

Two events or entities are “associated” with one another if one or more features of the first (e.g., its presence, level, activity, and/or form) are correlated with a feature of the second. For example, a first entity (e.g., a CDK7), gene expression profile, genetic signature (i.e., a single or combined group of genes in a cell with a uniquely characteristic pattern of gene expression), metabolite, or event (e.g., loss of cell cycle control in CDK7-positive cells)) is associated with a particular disease, if its presence, level, activity, and/or form correlates with the incidence of, severity of, and/or susceptibility to the disease (e.g., a cancer disclosed herein). Associations are typically assessed across a relevant population. Two or more entities are physically “associated” with one another if they interact, directly or indirectly, so that they are and/or remain in physical proximity with one another in a given circumstance (e.g., within a cell maintained under physiological conditions (e.g., within cell culture) or within a pharmaceutical composition). Entities that are physically associated with one another can be covalently linked to one another or non-covalently associated by, for example, hydrogen bonds, van der Waals forces, hydrophobic interactions, magnetism, or combinations thereof.

The terms “binding” and variants thereof (such as “bound” and “bind(s)”) refer to a covalent or non-covalent association of two or more entities (e.g., a compound and an agent within a pharmaceutical composition or a compound and its target within a cell). “Direct” binding or direct association occurs when the two entities physically contact one another (e.g., through a chemical bond) whereas indirect binding or indirect association occurs when one of the entities physically contacts one or more intermediate entities that bring the entities into physical proximity with one another (e.g., within a complex). Binding can be assessed in a variety of contexts (e.g., in full or partial isolation or in more complex, naturally occurring or model systems (e.g., in a tissue, organ, or cell in vivo or maintained in a tissue culture environment)).

The term “biologically active” describes an agent (e.g., a compound described herein) that produces an observable biological effect or result in a biological system or model thereof (e.g., in a human, other animal, or a system maintained in vitro). The “biological activity” can result from binding between the agent and a target (e.g., a CDK7), and it may result in modulation (e.g., induction, enhancement, or inhibition) of a biological pathway or event (e.g., a cellular activity (e.g., immunostimulation) or proliferation). The presence of biological activity and, optionally, its extent, can be assessed using known and/or standard methods to detect an immediate or downstream product or event associated with the biological activity, and any of the methods described herein can include a step of assessing such activity.

The term “biological sample” refers to a sample obtained or derived from a biological source of interest (e.g., a tissue or organism (e.g., an animal or human patient) or cell culture). The biological sample can contain a biological cell, tissue or fluid or any combination thereof. For example, a biological sample can be or can include ascites; blood; blood cells; bodily fluid(s), any of which may include or exclude cells; bone marrow; cerebrospinal fluid (CSF); feces; flexural fluid; free floating nucleic acids; gynecological fluids; immune infiltrates; lymph; peritoneal fluid; plasma; saliva; sputum; surgically-obtained specimens; tissue scraped or swabbed from the skin or a mucus membrane (e.g., in the nose, mouth, or vagina); tissue or fine needle biopsy samples; urine; washings or lavages such as a ductal lavage or broncheoalveolar lavage; or other body fluids, tissues, secretions, and/or excretions. A biological sample may include cancer cells or immune cells, such as NK cells and/or macrophages, which are found in many tissues and organs, including the spleen and lymph nodes. Cells (e.g., NK cells, macrophages, and cancer cells) within the sample may have been obtained from an individual for whom a treatment is intended. Samples used in the form in which they were obtained may be referred to as “primary” samples, and samples that have been further manipulated (e.g., by adding or removing one or more components to/from the sample) may be referred to as “secondary” or “processed” samples. Such processed samples can contain or be enriched for a particular cell type (e.g., a CDK7-expressing cell such as a macrophage or tumor cell), cellular component (e.g., a membrane fraction), or cellular material (e.g., one or more cellular proteins, including one or more of a CDK7, DNA, or RNA (e.g., mRNA), which may have been subjected to amplification).

The term “cancer” refers to a disease in which cells exhibit an aberrant growth phenotype characterized by loss of control of cell proliferation to an extent that will be detrimental to a patient having the disease; such cells can be referred to as a “cancer cell,” a “tumor cell,” or a “malignant cell.” A cancer can be classified by the type of tissue in which it originated (histological type) and/or by the primary site in the body in which the cancer first developed. Based on histological type, cancers are generally grouped into six major categories: carcinomas; sarcomas; myelomas; leukemias; lymphomas; and mixed types. A cancer treated as described herein can be of any one of these types and may comprise cells that are precancerous (e.g., benign), malignant, pre-metastatic, metastatic, and/or non-metastatic. A patient who has a malignancy or malignant lesion has a cancer. The present disclosure specifically identifies certain cancers to which its teachings may be particularly relevant, and one or more of these cancers may be characterized by a solid tumor or by a hematologic tumor, which may also be known as a blood cancer (e.g., of a type described herein).

The term “comparable” refers to two or more items (e.g., agents, entities, situations, sets of conditions, etc.) that are not identical to one another but are sufficiently similar to permit comparison therebetween so that one of ordinary skill in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. Comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. One of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more items to be considered comparable. For example, two items are comparable to one another when they have in common a sufficient number and type of substantially identical features to warrant a reasonable conclusion that any differences in results obtained or phenomena observed with the items are caused by or are indicative of the variation in those features that are varied. A comparable item can serve as a “control.” For example, a “control patient/population” can be an untreated patient/population who is afflicted with the same disease as a patient/population being treated.

The term “combination therapy” refers to those situations in which a patient is exposed to two or more therapeutic regimens (e.g., two or more therapeutic agents) to treat a single disease (e.g., a cancer). The two or more regimens may be administered simultaneously or sequentially (e.g., all “doses” of a first regimen are administered prior to administration of any dose(s) of a second regimen by the same or a different route of administration). For clarity, combination therapy does not require that individual agents be administered together in a single composition (or even necessarily at the same time), although in some embodiments, two or more agents (e.g., compounds described herein) may be administered together in a single composition or even as a combination compound (e.g., associated in a single chemical complex or covalent entity). In any of the compositions or methods described herein, a compound of Formula I can be a “first” agent.

The term “compound” means a chemical compound (e.g., a compound represented by a structural Formula depicted herein, a sub-genus thereof, or a species thereof). Any given compound can be biologically, therapeutically, or prophylactically active (e.g., when contained in a pharmaceutical composition in an effective amount) and can be provided and/or utilized (e.g., used in a biological assay, administered to a patient, incorporated into a medicament, or otherwise used as described herein) in any of a variety of forms.

A “disease” is a pathologic state regardless of whether the disease is commonly referred to as a condition, disorder, syndrome, or the like (e.g., a myeloproliferative disorder is a disease).

The terms “dosage form,” “formulation,” and “preparation” are used to refer to compositions containing a compound or other biologically and/or therapeutically active agent that is suitable for administration to a patient. The term “unit dosage form” refers to a physically discrete unit of a compound or other biologically and/or therapeutically active agent (e.g., a therapeutic or diagnostic agent) formulated for administration to a patient. Typically, each such unit contains a predetermined quantity of the active agent, which may be the amount prescribed for a single dose (i.e., an amount expected to correlate with a desired outcome when administered as part of a therapeutic regimen) or a fraction thereof. One of ordinary skill in the art will appreciate that the total amount of a therapeutic composition or agent administered to a particular patient is determined by one or more attending physicians and may involve administration of multiple unit dosage forms.

The term “dosing regimen” refers to the unit dosage form(s) administered to, or prescribed for, a patient, and typically includes more than one dose separated by periods of time (e.g., as described elsewhere herein). The dosage form(s) administered within a dosing regimen can be of the same unit dose amount or of different amounts. For example, a dosing regimen can comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount that is the same as or different from the first dose amount.

An “effective amount” of a compound of Formula (I) refers to an amount sufficient to elicit the desired biological response (e.g., treating or preventing the disease). As will be appreciated by one of ordinary skill in the art, the effective amount of a compound described herein may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the age and health of the patient. An effective amount encompasses therapeutic and prophylactic treatment. For example, in treating cancer, an effective amount of an inventive compound may reduce the tumor burden or stop the growth or spread of a tumor.

The term “excipient” refers to an adjuvant, carrier, diluent, or other vehicle with which a compound or composition described herein is administered or otherwise used. The excipient can be a sterile or sterilizable liquid, such as a water (e.g., water for injection), an aqueous solution (e.g., an isotonic salt solution (e.g., 0.9% NaCl), Ringer's solution, or a solution comprising 1,3-butanediol), or a natural or synthetic oil (e.g., a petroleum-based or mineral oil, an animal oil, or a vegetable oil (e.g., a peanut, soybean, sesame, or canola oil)). The oil may also be a nonvolatile oil of any animal or plant origin (i.e., a “fixed” oil). Sterile, fixed oils are conventionally employed as solvents and suspending media.

The excipient can be a solid; a liquid that includes one or more solid components (e.g., a salt, for example, a “normal saline”); a mixture of solids; or a mixture of liquids. The excipient may have characteristics that make it useful as a binding agent, buffering agent, diluent, disintegrating agent, dispersing agent, emulsifier, granulating agent, lubricating agent, preservative, or surface active agent. Excipients include, but are not limited to, alumina, aluminum stearate, a buffer (e.g., a phosphate salt (e.g., disodium hydrogen phosphate or potassium hydrogen phosphate) a sodium salt (e.g., sodium chloride), a zinc salt, or other salts or electrolytes), a cellulose-based substance (e.g., sodium carboxymethylcellulose), colloidal silica, glycine, an ion exchanger, lecithin, polyethylene glycol, potassium sorbate, protamine sulfate, a serum protein (e.g., human serum albumin), sorbic acid, a partial glyceride mixture of saturated vegetable fatty acids, magnesium trisilicate, polyvinyl pyrrolidone, a polyethylene-polyoxypropylene-block polymer, a polyacrylate, water, wax, and wool fat.

The term “hydrate” refers to a compound that is bound to water. The amount of water contained in the hydrate can be expressed as a ratio of the number of water molecules to the number of compound molecules. Thus, a hydrate of a compound may be represented by a general formula such as R·x H₂O, where R is the compound and x is a number greater than 0. For example, where x is 1, the hydrate is a monohydrate; where x is 0.5, the hydrate is a hemihydrate; where x is 2, the hydrate is a dihydrate; and where x is 6, the hydrate is a hexahydrate. A hydrate is a type of solvate.

“Improve(s),” “increase(s)” or “reduce(s)/decrease(s)” are terms used to characterize the manner in which a value has changed relative to a reference value. For example, a measurement obtained from a patient (or a biological sample obtained therefrom) prior to treatment can be increased or reduced/decreased relative to that measurement obtained during or after treatment in the same patient, a control patient, on average in a patient population, or biological sample(s) obtained therefrom. The value may be improved in either event, depending on whether an increase or decrease is associated with a positive therapeutic outcome.

The term “inhibitor” refers to an agent, including a compound described herein, whose presence (e.g., at a certain level or in a certain form) correlates with a decrease in the expression or activity of another agent (i.e., the inhibited agent or target) or a decrease in the occurrence of an event (e.g., tumor progression or metastasis). In some embodiments, an inhibitor exerts its influence on a target by binding to the target, directly or indirectly. In other embodiments, an inhibitor exerts its influence by binding and/or otherwise altering a regulator of the target, so that the expression and/or activity of the target is reduced. Inhibition can be assessed in silico, in vitro (e.g., in a cell, tissue, or organ culture or system), or in vivo (e.g., in a patient or animal model).

An “isotopic form” of a compound described herein (e.g., a compound of Formula (I)) is a form in which one or more elements of the compound have been replaced with an isotopic variant of that element. Where a compound contains an isotopic substitution, it can be, e.g., ²H or ³H for H; ¹¹C, ¹³C or ¹⁴C for ¹²C; ¹³N or ¹⁵N for ¹⁴N; ¹⁷O or ¹⁸O for ¹⁶O; ³⁶Cl for ³⁵C; ¹⁸F for ¹⁹F; ¹³¹I for ¹²⁷I; etc. Such compounds have use, for example, as analytical tools, as probes in biological assays, and/or as therapeutic or prophylactic agents for use in accordance with the present invention. In particular, an isotopic substitution of deuterium (2H) for hydrogen is known to potentially slow down metabolism, shift metabolism to other sites on the compound, slow down racemization and/or have other effects on the pharmacokinetics of the compound that may be therapeutically beneficial. In particular, deuterated forms of a compound described herein (or other forms thereof, such as salts or solvates) are embodiments of the present invention; such forms include deuterium in place of one or more of the hydrogen atoms in the compound but no other isotopic variants (e.g., no isotopes of ¹²C, ¹⁴N, or ¹⁸O).

The terms “neoplasm” and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue in which the growth of the mass surpasses and is not coordinated with the growth of a normal tissue. A neoplasm or tumor may be “benign” or “malignant” depending on the following characteristics: the degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis. A “benign neoplasm” is generally well differentiated, has a slower growth rate than a malignant neoplasm, and remains localized to the site of origin (i.e., does not have the capacity to infiltrate, invade, or metastasize to distant sites). Benign neoplasms include, but are not limited to, acrochordons, adenomas, chondromas, intraepithelial neoplasms, lentigos, lipoma, sebaceous hyperplasias, seborrheic keratoses, and senile angiomas. The benign neoplasm can also be tuberous sclerosis, or tuberous sclerosis complex (TSC) or epiloia (derived from “epilepsy, low intelligence, adenoma sebaceum”). Benign neoplasms can later give rise to malignant neoplasms (believed to occur as a result of genetic changes in a subpopulation of the tumor's neoplastic cells), and such neoplasms are referred to as “pre-malignant neoplasms.” An exemplary pre-malignant neoplasm is a teratoma. In contrast, a “malignant neoplasm” is generally poorly differentiated (anaplasia) and grows rapidly with progressive infiltration, invasion, and destruction of surrounding tissue. Malignant neoplasms also generally have the capacity to metastasize to distant sites.

A “patient” is any organism to which a compound described herein (or any variant thereof, as also described herein (e.g., a salt or solvate) is administered in accordance with the present invention e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical patients include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans; birds; insects; worms; etc.). A patient can be suffering from a disease described herein (e.g., a proliferative disease, such as cancer or a benign neoplasm).

A “pharmaceutical composition” is a composition in which an active agent (e.g., an active pharmaceutical ingredient (e.g., a compound described herein)) is formulated together with one or more pharmaceutically acceptable excipients. The active agent can be present in a unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to patients of a relevant population. The pharmaceutical composition may be specially formulated for administration in solid or liquid form, including forms made for oral or parenteral (e.g., intravenous) administration. For parenteral administration, the composition can be formulated, for example, as a sterile solution or suspension for subcutaneous, intramuscular, intravenous, intra-arterial, intraperitoneal, or epidural injection. Pharmaceutical compositions comprising an active agent (e.g., a compound described herein) can also be formulated as sustained-release formulations or as a cream, ointment, controlled-release patch, or spray for topical application. Creams, ointments, foams, gels, and pastes can also be applied to mucus membranes lining the nose, mouth, vagina, and rectum. Any of the compounds described herein and any pharmaceutical composition containing such a compound may also be referred to as a “medicament.”

The term “pharmaceutically acceptable,” when applied to an excipient used to formulate a composition disclosed herein (e.g., a pharmaceutical composition), means an excipient that is compatible with the other ingredients of the composition and not prohibitively deleterious to a patient (e.g., it is sufficiently non-toxic in the amount required and/or administered (e.g., in a unit dosage form). When applied to a salt (e.g., a salt of a compound described herein), “pharmaceutically acceptable” refers to the salt form of a compound that is, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without prohibitive toxicity, irritation, allergic response and the like, and that is commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art (see, e.g., Berge et al., J. Pharmaceutical Sciences, 66:1-19, 1977). Pharmaceutically acceptable salts of the compounds described herein include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N⁺(C₁₋₄ alkyl)₄ ⁻ salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as lower alkyl sulfonate, aryl sulfonate, carboxylate, halide, hydroxide, nitrate, phosphate, and sulfate.

When applied to a composition (e.g., a pharmaceutical composition), the term “pharmaceutically acceptable” indicates that the composition is suitable for administration to a patient by virtue of being non-contaminated (e.g., sterile) and non-toxic (i.e., generally safe; not expected to be poisonous).

A “prophylactically effective amount” of a compound described herein is an amount sufficient to delay the onset of a disease for a period of time that is substantially longer than expected (e.g., as evidenced by the absence of the signs and symptoms associated with the disease). A prophylactically effective amount can be an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent (a “second” prophylactic agent (e.g., a “second” compound)).

A “proliferative disease” is a disease that occurs due to abnormal growth or extension by the multiplication of cells (Walker, Cambridge Dictionary of Biology; Cambridge University Press: Cambridge, UK, 1990). A proliferative disease can be associated with the pathological proliferation of normally quiescent or normally dividing cells; the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); the pathological expression of proteolytic enzymes such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); and/or pathologic angiogenesis, as occurs in proliferative retinopathies and tumor metastases. Exemplary proliferative diseases include cancers, which may also be referred to as “malignant neoplasms,” benign neoplasms, and pathologic angiogenesis.

A “sign or symptom is reduced” when one or more objective signs or subjective symptoms of a disease are reduced in magnitude (e.g., intensity, severity, etc.) and/or frequency. A delay in the onset of a particular sign or symptom is one form of reducing the frequency of that sign or symptom. Reducing a sign or symptom can be achieved by, e.g., a “therapeutically active” compound optionally administered in an effective amount, as described herein.

The term “solvate” refers to a compound bound to a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding. Solvents that can be used in the reaction include water, methanol, ethanol, acetic acid, DMSO (dimethyl sulfoxide), THF (tetrahydrofuran), diethyl ether, and the like. A compound of Formula I or (Ia) can be prepared, e.g., in crystalline form, and then solvated. The solvate can be pharmaceutically acceptable and can be either a stoichiometric or non-stoichiometric solvate. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. “Solvate” encompasses both solution-phase and isolable solvates, and representative solvates include hydrates, ethanolates, and methanolates.

The term “specific,” as used herein with reference to an agent (e.g., a compound) having an activity (e.g., inhibition of a target), means that the agent discriminates between potential target entities or states. For example, an agent binds “specifically” to its intended target (or otherwise specifically inhibits its target) if it preferentially binds or otherwise inhibits the expression or activity of that target in the presence of one or more alternative targets. Although the invention is not so limited, a specific and direct interaction can depend upon recognition of a particular structural feature of the target (e.g., an epitope, a cleft, or a binding site). Specificity need not be absolute; the degree of specificity need only be enough to result in an effective treatment without unacceptable side effects. The specificity of an agent can be evaluated by comparing the effect of the agent on an intended target or state relative to its effect on a distinct target or state. The effects on the intended and distinct targets can each be determined or the effect on the intended target can be determined and compared to a reference standard developed at an earlier time (e.g., a reference specific binding agent or a reference non-specific binding agent). In some embodiments, the agent does not detectably bind the competing alternative target under conditions in which it detectably (and, preferably, significantly) binds its intended target and/or does not detectably inhibit the expression or activity of the competing target under conditions in which it detectably (and, preferably, significantly) inhibits the expression or activity of its intended target. A compound of the invention may exhibit, with respect to its target(s), a higher on-rate, lower off-rate, increased affinity, decreased dissociation, and/or increased stability compared with the competing alternative target, and any of these parameters can be assessed in methods of the invention.

As used herein with regard to a compound, the term “stable,” means the compound is not rendered inactive or substantially inactive when it is subjected to conditions that allow for its production, detection, recovery, purification, or use as described herein.

The invention encompasses “stereoisomeric forms” of a compound described herein (e.g., an optical and/or structural isomer). The stereoisomers of any referenced or depicted structure can be enantiomers and diastereomers (e.g., cis trans isomers and conformational isomers). These include the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformational isomers. Compositions containing a single type of stereochemical isomer as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Where a particular enantiomer is preferred, it can be provided substantially free of the corresponding enantiomer, and may also be referred to as “optically enriched,” meaning that the compound is made up of a significantly greater proportion of one enantiomer. For example, a plurality of the compound molecules can be made up of at least about 90% by weight of the preferred enantiomer (e.g., at least about 95%, 98%, or 99% by weight). Preferred enantiomers can be isolated from racemic mixtures by methods known in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts. They can also be prepared by asymmetric syntheses. If needed, one could consult, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, Tables of Resolving Agents and Optical Resolutions p. 268 (E.L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, Ind. 1972).

The term “substantially” refers to the qualitative condition of exhibiting a characteristic or property of interest to a total or near-total extent or degree. One of ordinary skill in the art will understand that biological and chemical phenomena rarely, if ever, go to completion and/or proceed to completeness or achieve or avoid an absolute result. The term “substantially” may therefore be used to capture the potential lack of completeness inherent in many biological and chemical phenomena. For example, a chemical reaction may be characterized as substantially complete even though the yield is well below 100%. Certain features may also be deemed “substantially identical” when they are about the same and/or exhibit about the same activity. For example, two nearly identical compounds that produce about the same effect on an event (e.g., cellular proliferation) may be described as substantially similar. With regard to the purity of a compound or composition, “substantially pure” is defined below.

The term “substantially pure,” when used to refer to a compound described herein, means that a preparation of the compound is more than about 85% (w/w) compound (e.g., more than about 90%, 95%, 97%, 98%, 99%, or 99.9%).

An individual who is “susceptible to” a disease (e.g., a proliferative disease, such as cancer) has a greater than average risk for developing the disease. Such an individual may not yet display any symptoms of the disease and may not have not been diagnosed with the disease. Such an individual may have been exposed to conditions associated with development of the disease (e.g., exposure to a carcinogen). Susceptibility can be assessed by one of ordinary skill in the art and can be determined relative to a population-based risk.

The term “tautomer” refers to a structural or constitutional isomer of a compound; tautomers are compounds having the same molecular formula but different atomic organization and bonding patterns. Tautomeric compounds readily interconvert and vary from one another in the displacement of hydrogen atoms and electrons. Thus, two tautomeric compounds may be in equilibrium through the movement of π electrons and an atom (usually H). For example, enols and ketones are tautomers because they are rapidly interconverted by treatment with either acid or base. Tautomeric compounds may exhibit improved chemical reactivity and biological activity relative to the comparable non-tautomeric compound.

A “therapeutic regimen” refers to a dosing regimen that, when administered across a relevant population, is correlated with a desired therapeutic outcome.

The term “treatment,” and linguistic variants thereof, such as “treat(s)” and “treating,” refer to any use of a compound or pharmaceutical composition described herein to partially or substantially completely alleviate, ameliorate, relieve, inhibit, reduce the severity of, and/or reduce the incidence of one or more signs or symptoms of a particular disease (e.g., a proliferative disease such as cancer). The patient being treated (or who has been identified as a candidate for treatment) may exhibit only early signs or symptoms of the disease or may exhibit one or more established or advanced signs or symptoms of the disease. “Treatment” is distinguished from “prophylaxis,” which relates to delaying the onset of one or more signs or symptoms of a disease. In that case, the patient may not exhibit signs and/or symptoms of the disease and/or may be known to have one or more susceptibility factors that are statistically correlated with increased risk of development of the relevant disease. However, once a patient exhibits signs or symptoms of a disease and has been treated, treatment may be continued to delay or prevent recurrence.

A “therapeutically effective amount” of a compound described herein is an amount sufficient to treat a disease in a population of patients. A therapeutically effective amount is an amount that provides a therapeutic benefit in the treatment of a disease (e.g., by treating one or more signs or symptoms associated with the disease). A therapeutically effective amount of a compound described herein can also be an amount that enhances the therapeutic efficacy of another therapeutic agent (a “second” therapeutic agent (e.g., a “second” compound)).

The terms “neoplasm” and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated with the growth of a normal tissue. A neoplasm or tumor may be “benign” or “malignant,” depending on the following characteristics: degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis. A “benign neoplasm” is generally well differentiated, has characteristically slower growth than a malignant neoplasm, and remains localized to the site of origin. In addition, a benign neoplasm does not have the capacity to infiltrate, invade, or metastasize to distant sites. Exemplary benign neoplasms include, but are not limited to, lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheic keratoses, lentigos, and sebaceous hyperplasias. In some cases, certain “benign” tumors may later give rise to malignant neoplasms, which may result from additional genetic changes in a subpopulation of the tumor's neoplastic cells, and these tumors are referred to as “pre-malignant neoplasms.” An exemplary pre-malignant neoplasm is a teratoma. In contrast, a “malignant neoplasm” is generally poorly differentiated (anaplasia) and has characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant neoplasm generally has the capacity to metastasize to distant sites.

The details of one or more embodiments of the invention are set forth herein. Other features, objects, and advantages of the invention will be apparent from the Detailed Description, the Figures, the Examples, and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a Table disclosing exemplary compounds of the invention.

FIG. 2 is a Table disclosing further exemplary compounds of the invention.

FIG. 3 is a Table providing additional details of the synthesis of certain compounds of the invention, as well as their NMR and MS values.

DETAILED DESCRIPTION

In one aspect of the present invention, provided are compounds of formula (I):

or a pharmaceutically acceptable salt, solvate (e.g., hydrate), tautomer, stereoisomer, or isotopic form thereof, wherein:

ring A is:

ring B is:

wherein each of R², R³, R⁴ and R⁵ are, independently, hydrogen or —CH₃;

X and Y are, independently, N or CH;

R¹ is hydrogen or fluoro; and

wherein the compound is other than:

In some embodiments, ring A is:

In more specific embodiments, ring A is

In even more specific embodiments, ring A is

In some embodiments, ring A is

In some embodiments, ring B is:

In some embodiments, ring B is:

In some embodiments, ring B is:

In various embodiments of Formula I: R¹ is hydrogen; R¹ is fluoro; X is CH and Y is CH; X is N and Y is CH; X is N and Y is N; R² and R³ is hydrogen; each of R⁴ and R⁵ are —CH₃; R⁴ is hydrogen and R⁵ is —CH₃.

Also described herein are compounds of Formula II:

and pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, stereoisomers, and isotopic forms thereof, wherein:

ring A is:

and

R¹ is selected from hydrogen and fluoro.

In some embodiments of a compound of Formula II, ring A is:

In more specific embodiments, ring A is:

In even more specific embodiments, ring A is:

In some embodiments of Formula II, ring A is

In various embodiments of Formula II: R¹ is hydrogen; R¹ is fluoro.

The compound can be selected from any of the compounds in the Table of FIG. 1 or the Table of FIG. 2 or can be a pharmaceutically acceptable salt, solvate (e.g., hydrate), tautomer, stereoisomer, or isotopic form thereof.

Any compound described herein can be prepared using methods described herein and/or known in the art. Techniques useful in synthesizing these compounds are accessible to one of ordinary skill in the art, and the discussion below illustrates certain of the diverse methods available for use in assembling them. The discussion is not intended to limit the scope of useful reactions or reaction sequences. Any pharmaceutical composition described herein can be prepared by methods known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the compound (e.g., a compound of formula (I); the “active ingredient”) into association with an excipient and/or one or more other accessory ingredients or “second” agents, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit and/or packaging the composition within a kit.

Compounds and/or other compositions provided herein (e.g., pharmaceutical compositions) have a variety of uses, including in research and/or clinical settings (e.g., in methods of providing a diagnosis or prognosis and in prophylactic or therapeutic treatment methods).

In some embodiments, a provided compound and/or composition is considered to be specific for a given kinase or set of kinases when it shows at least or about 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold or more activity for the specific kinase(s) than for one or more appropriate comparator kinase(s) (e.g., for CDK7 relative to one or more of CDK2, CDK9, and/or CDK12). One of ordinary skill in the art will recognize the evaluating specificity in terms of “fold difference” is only one applicable measure. For example, specificity can be expressed as a “percent difference.” For example, a provided compound and/or composition is considered to be specific for CDK7 when it shows at least 101%, 105%, 110%, 120%, 130%, 140%, 150%, 200%, 300%, 400%, 500% or more activity for CDK7 than for one or more of CDK2, CDK9, and/or CDK12.

Compounds of the present disclosure can be prepared and administered in a wide variety of oral and parenteral dosage forms. Thus, the compounds of the present disclosure can be formulated for administration by injection (e.g. intravenously, intramuscularly, intracutaneously, subcutaneously, or intraperitoneally). The compounds can also be formulated for administration by inhalation (e.g., intranasally) or by insufflation. In other embodiments, the compounds described herein can be formulated for topical or transdermal administration (i.e., they can be in a dosage form suitable for administration by the various routes just described).

For preparing pharmaceutical compositions including a compound described herein, pharmaceutically acceptable carriers can be added in either solid or liquid form or a combination thereof. Solid dosage form preparations within the scope of the present invention include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules. A solid carrier can be a substance that may also act as a diluent, flavoring agent, binder, preservative, tablet disintegrating agent, or an encapsulating material. In powders, the carrier is a finely divided solid in a mixture with the finely divided active component (e.g., a compound described herein, e.g., a compound conforming to the structure of Formula II). In tablets, the active component is mixed with the carrier having the necessary binding properties in suitable proportions and compacted in the shape and size desired. Pharmaceutical compositions, including those formulated as powders and tablets, can contain from about 5% to about 70% of the active compound. Suitable carriers are magnesium carbonate, magnesium stearate, talc, sugar, lactose, pectin, dextrin, starch, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose, a low melting wax, cocoa butter, and the like. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration. For preparing suppositories, a low melting wax, such as a mixture of fatty acid glycerides or cocoa butter, is melted and the active component is dispersed therein.

Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions. For parenteral injection, liquid preparations can be formulated in solution in aqueous polyethylene glycol solution. When parenteral application is needed or desired, particularly suitable admixtures for the compounds of the invention are injectable, sterile solutions, preferably oily or aqueous solutions, as well as suspensions, emulsions, or implants, including suppositories. In some embodiments, suitable carriers for parenteral administration will be selected for human administration.

In particular, carriers for parenteral administration include aqueous solutions of dextrose, saline, pure water, ethanol, glycerol, glycerol formal, polyethylene glycol, propylene glycol, peanut oil, sesame oil, polyoxyethylene-block polymers, pyrrolidine, N-methyl pyrrolidione, and the like. Ampoules are convenient unit dosage forms. The compounds of the present disclosure can also be incorporated into liposomes or administered via transdermal pumps or patches. Pharmaceutical admixtures suitable for use in the present disclosure include those described, for example, in Pharmaceutical Sciences (17th Ed., Mack Pub. Co., Easton, Pa.) and WO 96/05309, the teachings of both of which are hereby incorporated by reference.

Aqueous solutions suitable for oral use can be prepared by dissolving the active component in water and adding suitable colorants, flavors, stabilizers, and thickening agents as desired. Aqueous suspensions suitable for oral use can be made by dispersing the finely divided active component in water with viscous material, such as natural or synthetic gums, resins, methylcellulose, sodium carboxymethylcellulose, and other well-known suspending agents.

Also included are solid form preparations that are intended to be converted, shortly before use, to liquid form preparations for oral administration. Such liquid forms include solutions, suspensions, and emulsions. These preparations may contain, in addition to the active component, colorants, flavors, stabilizers, buffers, artificial and natural sweeteners, dispersants, thickeners, solubilizing agents, and the like.

The pharmaceutical compositions are preferably in unit dosage form. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Unit dosage forms can also be capsules, tablets, cachets, lozenges, or the appropriate number of any of these in packaged form.

The quantity of active component in a unit dose preparation may be varied or adjusted from 0.1 mg to 10000 mg, more typically 1.0 mg to 1000 mg, most typically 10 mg to 500 mg, according to the particular application and the potency of the active component. The composition can, if desired, also contain other compatible therapeutic agents.

Some compounds may have limited solubility in water and therefore may require a surfactant or other appropriate co-solvent in the composition (e.g., polysorbate 20, 60, and 80; Pluronic® F-68, F-84, and P-103; cyclodextrin; and polyoxyl 35 castor oil). Such co-solvents are typically employed at a level between about 0.01% and about 2% by weight.

Viscosity greater than that of simple aqueous solutions may be desirable to decrease variability in dispensing the formulations, to decrease physical separation of components of a suspension or emulsion of formulation, and/or otherwise to improve the formulation. Such viscosity building agents include, for example, polyvinyl alcohol, polyvinyl pyrrolidone, methyl cellulose, hydroxy propyl methylcellulose, hydroxyethyl cellulose, carboxymethyl cellulose, hydroxy propyl cellulose, chondroitin sulfate and salts thereof, hyaluronic acid and salts thereof, and combinations of the foregoing. Such agents are typically employed at a level between about 0.01% and about 2% by weight.

Compositions of the present invention may additionally include components to provide sustained release and/or comfort (e.g., high molecular weight, anionic mucomimetic polymers, gelling polysaccharides, and finely-divided drug carrier substrates). These components are discussed in detail in U.S. Pat. Nos. 4,911,920; 5,403,841; 5,212,162; and 4,861,760. The entire contents of these patents are incorporated herein by reference in their entirety for all purposes.

Pharmaceutical compositions provided by the present disclosure include compositions wherein the active ingredient is contained in a therapeutically effective amount, i.e., in an amount effective to achieve its intended purpose. The actual amount effective for a particular application will depend, inter alia, on the condition being treated. For example, when administered in methods to a subject with cancer, such compositions will contain an amount of active ingredient effective to achieve the desired result.

The dosage and frequency (single or multiple doses) of compound administered can vary depending on a variety of factors, including route of administration; the size, age, sex, health, body weight, body mass index, and diet of the recipient; nature and extent of symptoms of the disease being treated; any concurrent treatment; and complications from any disease or treatment regimen. Other therapeutic regimens or agents can be used in conjunction with the methods and compounds of the present disclosure.

For any compound, any variant form thereof (e.g., any salt or solvate), or any pharmaceutical composition described herein, the therapeutically effective amount can be initially determined from, or informed by data generated in, cell culture assays and/or animal models of disease. For example, a dose for humans can be formulated to achieve a concentration that has been found to be effective in animals. The dosage in humans can be adjusted by, for example, monitoring kinase (CDK7) inhibition, the signs an symptoms of the disease being treated, and side effects and subsequently adjusting the dosage upwards or downwards.

Dosages may be varied depending upon the requirements of the patient and the compound being employed. The dose administered to a patient should be sufficient to effect a beneficial therapeutic response in the patient over time. The size of the dose also will also be determined by the existence, nature, and extent of any adverse side effects. Generally, treatment is initiated with smaller dosages, which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under a desired circumstance is reached. In some embodiments, the concentration of compound is about 0.001% to 10% w/v (e.g., about 0.1% to about 5% w/v). In some embodiments, the concentration range is 0.1% to 5% w/v. Concentrations, dosage amounts, and intervals can be adjusted in each individual patient to provide levels of the administered compound effective for the particular disease being treated. This will provide a therapeutic regimen commensurate with the severity of the patient's disease.

Methods of Treatment and Uses: The disease to be treated or prevented using the compounds of Formula (I), pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, stereoisomers, isotopically labeled derivatives thereof, or compositions containing any of the foregoing will typically be associated with aberrant expression or activity of CDK7. For example, a gene encoding CDK7 can be overexpressed or misexpressed (i.e., expressed at abnormally high levels in a tissue where it is normally expressed; expressed or overexpressed in a tissue where it is not normally expressed; or expressed at a time during which it is not normally expressed). The activity of the encoded protein can also be increased, and aberrant expression or activity can be relative to the expression or activity in a comparable patient, population of patients, biological sample, or plurality of biological samples that do not manifest signs or symptoms of the disease in question. Both expression and activity may be abberant, or only activity may be abberant.

Methods of testing patients and biological samples for levels of CDK7 expression or activity are within the scope of the invention and may be performed prior to, during, or after treatment as described herein. CDK7 levels can be tested and compared between healthy patients and patients having a disease; between treated and untreated patients; between biological samples from healthy tissues and diseased tissues (whether treated or untreated); and between biological samples that represent models of a disease disclosed herein. Although no aspect of the invention is limited by the cellular mechanisms that result from contacting a cell described herein (whether in a patient or a biological sample ex vivo) with a compound or other composition described herein, this contact may cause cytotoxicity via induction of apoptosis, and assessing cytotoxicity can be a part of the methods of testing patients and biological samples prior to, during, or after treatment.

As noted, the proliferative disease to be treated or prevented using the compounds described herein or pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, stereoisomers, isotopically labeled derivatives, and compositions thereof include the cancers described herein, particularly when a given cancer is known to be or found to be associated with aberrant CDK7 expression or activity. The proliferative disease can be a cancer associated with dependence on BCL-2 anti-apoptotic proteins (e.g., MCL-1 and/or XIAP); with overexpression of MYC; with overexpression of CDK18; with overexpression of CDK19; with overexpression of FGFR1; with overexpression of CDK6; with overexpression of CCND2; or with overexpression of CDKN2A. In certain embodiments, the proliferative disease is a cancer associated with the absence of, or suppression of, a wild-type RB1 gene.

In certain embodiments, the proliferative disease is a blood cancer, which may also be referred to as a hematopoietic or hematological cancer or malignancy. More specifically and in various embodiments, the blood cancer can be a leukemia such as acute lymphocytic leukemia (ALL; e.g., B cell ALL or T cell ALL), acute myelocytic leukemia (AML; e.g., B cell AML or T cell AML), chronic myelocytic leukemia (CML; e.g., B cell CML or T cell CML), chronic lymphocytic leukemia (CLL; e.g., B cell CLL (e.g., hairy cell leukemia) or T cell CLL), chronic neutrophilic leukemia (CNL), or chronic myelomonocytic leukemia (CMML). The blood cancer can also be a lymphoma such as Hodgkin lymphoma (HL; e.g., B cell HL or T cell HL), non-Hodgkin lymphoma (NHL; e.g., B cell NHL or T cell NHL), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), a marginal zone B cell lymphoma (e.g., splenic marginal zone B cell lymphoma), primary mediastinal B cell lymphoma (e.g., splenic marginal zone B cell lymphoma), primary mediastinal B cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (i.e., Waldenstrom's macroglobulinemia), immunoblastic large cell lymphoma, precursor B lymphoblastic lymphoma, or primary central nervous system (CNS) lymphoma. The B cell NHL can be diffuse large cell lymphoma (DLCL; e.g., diffuse large B cell lymphoma), and the T cell NHL can be precursor T lymphoblastic lymphoma or a peripheral T cell lymphoma (PTCL). In turn, the PTCL can be a cutaneous T cell lymphoma (CTCL) such as mycosis fungoides or Sezary syndrome, angioimmunoblastic T cell lymphoma, extranodal natural killer T cell lymphoma, enteropathy type T cell lymphoma, subcutaneous anniculitis-like T cell lymphoma, or anaplastic large cell lymphoma. While the invention is not limited to treating or preventing blood cancers having any particular cause or presentation, stem cells within the bone marrow may proliferate, thereby becoming a dominant cell type within the bone marrow and a target for a compound described herein. Leukemic cells can accumulate in the blood and infiltrate organs such as the lymph nodes, spleen, liver, and kidney. In some embodiments, a compound of the present disclosure is useful in the treatment or prevention of a leukemia or lymphoma.

In other embodiments, the proliferative disease is characterized by a solid tumor considered to be either of its primary location or metastatic. Exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy (also known as monoclonal gammopathy of unknown significance (MGUS); biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, or medullary carcinoma of the breast, any of which may be present in subjects having a particular profile, such as an HR+ (ER+ or PR+), HR− (having neither estrogen nor progesterone receptors), a triple negative breast cancer (TNBC; ER−/PR−/HER2−), or a triple-positive breast cancer); brain cancer (e.g., meningioma, glioblastoma, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma, or neuroblastoma); bronchus cancer; carcinoid tumor carcinoid tumor, which may be benign; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer, or colorectal adenocarcinoma); connective tissue cancer; epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma or multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterine cancer or uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of the esophagus or Barrett's adenocarcinoma; Ewing's sarcoma (or other pediatric sarcoma, such as embryonal rhabdomyosarcoma or alveolar rhabdomyosarcoma); eye cancer (e.g., intraocular melanoma or retinoblastoma); familial hypereosinophilia; gallbladder cancer; gastric cancer (e.g., stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germ cell cancer; head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma)), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)); hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreatic neuroendocrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g., pancreatic adenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of the penis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplastic syndromes; intraepithelial neoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)); small bowel cancer or small intestine cancer (e.g., appendix cancer); soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; testicular cancer (e.g., seminoma, testicular embryonal carcinoma); thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).

The proliferative disease can be associated with pathologic angiogenesis, and the methods of the invention (and uses of the compounds and other compositions described herein) encompass inhibiting pathologic angiogenesis in the context of cancer treatment.

As noted, the patient for which administration is contemplated includes, but is not limited to, a human (i.e., a male, female or transgendered person of any age group, e.g., a pediatric patient (e.g., infant, child, adolescent) or adult patient (e.g., young adult, middle-aged adult, or senior adult)) and/or other non-human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys). Thus, the patient may be a domesticated animal. The non-human animal may be a transgenic animal (e.g., an animal valuable in research, such as a transgenic mouse or transgenic pig).

A cell used or treated as described herein may be a healthy cell or an unhealthy or abnormal cell (e.g., a cancer cell, tumor cell, or other cell that is proliferating uncontrollably). A compound of the invention may be administered to any such cell in vitro or in vivo. In various embodiments, the cell is: a cancer cell; a tumor cell; a proliferating cell; a blood cell (e.g., a lymphocyte); an endothelial cell; or an immune cell. In various embodiments, the cancer cell is: a leukemia cell; a CLL cell; a CMML cell; an AML cell; a breast cancer or ovarian cancer cell; a melanoma cell; a multiple myeloma cell; or a cell of any other cancer or disease disclosed herein.

In certain embodiments, the methods described herein comprise the additional step of administering one or more additional pharmaceutical agents in combination with the compound of formula (I) a pharmaceutically acceptable salt thereof, or compositions comprising such compound or pharmaceutically acceptable salt thereof. Such additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-diabetic agents, anti-inflammatory agents, immunosuppressant agents, and a pain-relieving agent. The additional pharmaceutical agent(s) may synergistically augment inhibition of CDK7 induced by the inventive compounds or compositions of this invention in the biological sample or subject. Thus, the combination of the inventive compounds or compositions and the additional pharmaceutical agent(s) may be useful in treating proliferative diseases resistant to a treatment using the additional pharmaceutical agent(s) without the inventive compounds or compositions.

As indicated, the present invention provides the compounds described herein (e.g., a compound of Formula (I)) and pharmaceutically acceptable salts, solvates (e.g., hydrates), tautomers, isotopic forms, and compositions thereof (e.g., pharmaceutical compositions), for use in the treatment of a proliferative disease or any other disease described herein in a patient. While the compounds, variants thereof, compositions containing them, and methods of use are not limited according to the underlying mechanism of action, we note that use may result in an inhibition of cell growth by, for example, promoting apoptosis or altering the expression or activity of disease-related genes.

EXAMPLES

The compounds provided herein can be prepared from readily available starting materials using modifications to the specific synthesis protocols set forth below that would be well known to those of skill in the art. It will be appreciated that where typical or preferred process conditions (i.e., reaction temperatures, times, mole ratios of reactants, solvents, pressures, etc.) are given, other process conditions can also be used unless otherwise stated. Optimum reaction conditions may vary with the particular reactants or solvents used, but such conditions can be determined by those skilled in the art by routine optimization procedures.

Additionally, as will be apparent to those skilled in the art, conventional protecting groups may be necessary to prevent certain functional groups from undergoing undesired reactions. The choice of a suitable protecting group for a particular functional group as well as suitable conditions for protection and deprotection are well known in the art. For example, numerous protecting groups, and their introduction and removal, are described in Greene et al., Protecting Groups in Organic Synthesis, Second Edition, Wiley, New York, 1991, and references cited therein.

Example 1. Synthesis of (S)-4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 104) Step 1: 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-1H-indole

To a solution of 2,4-dichloro-5-(trifluoromethyl)pyrimidine (4.87 g, 22.44 mmol) in dichloroethane (29 mL) was added aluminum trichloride (3.26 g, 24.49 mmol). The resulting suspension was stirred at 70° C. for 15 min to provide a clear yellow solution. Reaction mixture was then slightly cooled down (to 60° C.) followed by addition of 6-bromoindole (4.0 g, 20.40 mmol). The resulting orange solution was stirred at 80° C. for 2 h. The reaction mixture was cooled down to RT (room temperature), and ice-cold water was then added followed by stirring for 30 min. The resulting slurry was further diluted with EtOAc (ethyl acetate) and water, then filtered. Aqueous layer was extracted with EtOAc (twice), the organics were combined, dried over Na₂SO₄, and concentrated under vacuum. The crude red solid was dissolved in minimal amount of MeOH (methanol) and, after stirring for 30 min at RT, was then filtered to provide the desired regioisomer as a beige solid (2.20 g, 5.85 mmol, 29% yield). The product was used in the next step without further purification.

Step 2: 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole

To a solution of 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-1H-indole (1.19 g, 3.16 mmol) in dry THF (tetrahydrofuran; 15.8 mL) was added sodium tert-butoxide, 2 M in THF (1.90 mL, 3.79 mmol), and the resulting mixture was stirred for 30 min at 0° C. Benzenesulfonyl chloride (0.48 mL, 3.79 mmol) was then added. Reaction mixture was stirred for 15 min at 0° C. and then at RT for overnight. The mixture was diluted with EtOAc and washed with water. The organic phase was separated, dried over Na₂SO₄, and concentrated under vacuum to provide the crude title compound as a beige solid (1.40 g, 2.71 mmol, 86% yield). The product was used in the next step without further purification.

Step 3: (S)-6,6-dimethylpiperidin-3-amine

(S)-tert-Butyl (6-oxopiperidin-3-yl)carbamate (1.00 g, 4.67 mmol) (Tetrahedron Letters 36:8204, 1995) was dissolved in THF (47 mL), and the solution was cooled to −10° C. Zirconium(IV) chloride (2.61 g, 11.22 mmol) was added, and the mixture was stirred for 30 min at this temperature. Methylmagnesium bromide 3 M solution in ether (20.25 mL, 60.75 mmol) was added, and then reaction mixture was allowed to slowly warm up to RT and then stirred for overnight. The solution was quenched with 30% NaOH, diluted with EtOAc, filtered, and then extracted 3 times with EtOAc. The organics were combined, dried over Na₂SO₄, filtered, and concentrated under vacuum to provide crude product as a yellow oil that was used without further purification. The obtained oil was dissolved in DCM (dichloromethane; 47 mL) and TFA (trifluoroacetic acid; 3.58 mL, 46.73 mmol) was added. The reaction mixture was stirred at RT for 16 h. The mixture was concentrated under reduced pressure and co-evaporated for few times with DCM to provide a brown oil of crude title compound, which was used in the next step without further purification.

Step 4: (S)-4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole (1.40 g, 2.71 mmol) and crude (S)-6,6-dimethylpiperidin-3-amine from the previous step (4.67 mmol) in dry THF (21 mL) was added DIPEA (N,N-diisopropyl ethylamine; 1.42 mL, 8.13 mmol). The reaction mixture was then stirred at RT for 16 h. The reaction mixture was diluted with EtOAc and washed with water. Organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under vacuum to provide a yellow oil of crude product that was purified by reverse phase chromatography (C18, MeCN in aq. (aqueous) 10 mM ammonium bicarbonate, 30 to 100% gradient, where product was washed out from the column at 100% MeCN with 10 mL of IPA (isopropanol)). The title compound was obtained as a brown foam (330 mg, 0.54 mmol, 20% yield).

Step 5: (S)-4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)-4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (100 mg, 0.164 mmol) and (3,5-dimethylisoxazol-4-yl)boronic acid (69 mg, 0.493 mmol) in previously degassed 2:1 mixture of dioxane/H₂O (3 mL) was added Cs₂CO₃ (161 mg, 0.493 mmol), and the mixture was degassed for another 15 min. Then, Pd(PPh₃)₄ (19 mg, 0.016 mmol) was added, and the reaction mixture was stirred at 100° C. for 1.5 h. The mixture was allowed to cool down to RT, diluted with EtOAc and washed with water and brine. The organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient followed by 100% of IPA) to give the title compound as a yellowish oil (56 mg, 0.09 mmol, 55% yield).

Step 6: (S)-4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)-4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (56 mg, 0.09 mmol) in dioxane (1 mL) was added 5M aq. NaOH (0.18 mL, 0.90 mmol). The reaction mixture was stirred at 70° C. for 3 h. The mixture was then concentrated, and the residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium bicarbonate, 0 to 100% gradient) to provide the title compound as an off-white solid (26 mg, 0.052 mmol, 58% yield).

Example 2. Synthesis of (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(6-(thiazol-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 106) Step 1: (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(1-(phenylsulfonyl)-6-(thiazol-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)-4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-N-(6,6-dimethylpiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Example 1; 220 mg, 0.36 mmol) in toluene (3.6 mL) was added 2-(tributylstannyl)thiazole (169 mg, 0.45 mmol), and this suspension was degassed for 20 min. Bis(triphenylphosphine)palladium(II) dichloride (13 mg, 0.02 mmol) was then added, and the reaction mixture was stirred at 100° C. for 2 h. After cooling down to RT, the mixture was filtered through Celite, then diluted with water (20 mL) and EtOAc (30 mL) and basified with sat. (saturated) aq. NaHCO₃ (5 mL). Organic phase was separated, washed with water (20 mL) and brine (2×10 mL), dried over MgSO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (THF in hexanes, 0 to 100% gradient) to obtain the title compound as a yellow oil (101 mg, 0.16 mmol, 45% yield).

Step 2: (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(6-(thiazol-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(1-(phenylsulfonyl)-6-(thiazol-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (101 mg, 0.16 mmol) in dioxane (1.6 mL) was added 5M aq. NaOH (0.32 mL, 1.60 mmol), and the reaction mixture was stirred at 70° C. for 2 h. The mixture was then concentrated, and the residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 0 to 100% gradient) to obtain the title compound as a pale yellow solid (20.3 mg, 0.043 mmol, 27% yield).

Example 3. Synthesis of (S)-4-(6-(oxazol-2-yl)-1H-indol-3-yl)-N-(piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 110) and (S)-4-(6-(oxazol-5-yl)-1H-indol-3-yl)-N-(piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 111) Step 1: (S)-tert-butyl 3-((4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

A mixture of 1-(benzenesulfonyl)-6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]indole (Example 1, step 2; 1.00 g, 1.94 mmol, 1.00 eq), (S)-tert-butyl (3S)-3-aminopiperidine-1-carboxylate (388.54 mg, 1.94 mmol, 1.00 eq) and DIEA (N,N-diisopropylethylamine; 752.18 mg, 5.82 mmol, 1.02 mL, 3.00 eq) in NMP (N-methyl-2-pyrrolidone; 10.00 mL) was stirred at 140° C. for 1 hr. The mixture was diluted with water (100 mL) and extracted with EtOAc (50 mL×2). Combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered, and concentrated under reduced pressure to a yellow oil. The residue was purified by SiO₂ chromatography (PE/EtOAc, 10:1 to 5:1) to afford the title compound (1.13 g, 86%) as a yellow solid.

Step 2: (S)-tert-butyl 3-((4-(6-(oxazol-2-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate and (S)-tert-butyl 3-((4-(6-(oxazol-5-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a microwave vial, (S)-tert-butyl 3-((4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (150.0 mg, 0.220 mmol), pivalic acid (9.0 mg, 0.088 mmol), K₂CO₃ (91.4 mg, 0.661 mmol), Pd(OAc)₂ (2.5 mg, 0.011 mmol; 5 mol %), and RuPhos (2-dicyclohexylphosphino-2′,6′-diisopropoxybiphenyl; 10.3 mg, 0.022 mmol; 10 mol %) were added. The microwave vial was sealed under nitrogen. Dry, degassed toluene (1.0 mL) was then added followed by oxazole (29 μL, 0.441 mmol). The reaction mixture was stirred at 110° C. in an oil bath for 16 h. After cooling down to RT, the reaction mixture was concentrated, and the residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient) to give the title compounds: 23 mg (pale oil, 0.034 mmol, 16% yield) and 46 mg (pale oil, 0.069 mmol, 31% yield), correspondingly.

Step 3: (S)-4-(6-(oxazol-2-yl)-1H-indol-3-yl)-N-(piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)-tert-butyl 3-((4-(6-(oxazol-2-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (41 mg, 0.061 mmol) in dioxane (3 mL) was added 5M aq. NaOH (0.122 mL, 0.610 mmol), and the reaction mixture was stirred at 50° C. for 3 h. The mixture was cooled down to RT, diluted with MeTHF (2-methyltetrahydrofuran; 5 mL) and water (5 mL). Organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The obtained crude was then re-dissolved in DCM (2 mL), and TFA was added (0.187 mL, 2.440 mmol). The reaction mixture was stirred at RT for 1 h. The mixture was concentrated under reduced pressure and azeotroped for few times with DCM. The basified crude product was then purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 0 to 100% gradient) to obtain the title compound as an off-white solid (7.0 mg, 0.016 mmol, 27% yield).

Example 4. Synthesis of (S)-4-(6-(3-methylisoxazol-4-yl)-1H-indol-3-yl)-N-(piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 114) Step 1: (S)-tert-butyl 3-((4-(6-(3-methylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of (S)-tert-butyl 3-((4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (Example 3, step 1; 150 mg, 0.22 mmol) in degassed 2:1 mixture of dioxane/water (1.5 mL) were added NaHCO₃ (37 mg, 0.44 mmol) and 3-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)isoxazole (81 mg, 0.39 mmol), the resulted suspension was degassed for 15 min. Tetrakis(triphenylphosphine)pal-ladium(0) (25 mg, 0.02 mmol) was added, and the reaction mixture was stirred at 100° C. for 1 h. After cooling down to RT, the mixture was diluted with EtOAc (15 mL) and water (10 mL), the crude product was extracted with EtOAc (2×10 mL). The combined organic phase was washed with sat. aq. NaHCO₃ (5 mL), water (2×5 mL), and brine (2×10 mL), then dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient) to obtain the title compound as a yellow oil (139 mg, 0.20 mmol, 93% yield).

Step 2: (S)-tert-butyl 3-((4-(6-(3-methylisoxazol-4-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of (S)-tert-butyl 3-((4-(6-(3-methylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (139 mg, 0.20 mmol) in THF (2 mL) was added 1M TBAF (tetrabutylammonium fluoride) solution in THF (2 mL, 2.04 mmol), and the reaction mixture was stirred at 70° C. for 30 min. The mixture was then concentrated under vacuum, re-dissolved in MeTHF (5 mL) and washed with sat. aq. NH₄Cl (5×5 mL) and brine (5 mL). Organic phase was separated, dried over MgSO₄, filtered, and concentrated under reduced pressure to provide a yellow oil of crude title compound (111 mg, 0.20 mmol, quant. yield), which was used in the next step without further purification.

Step 3: (S)-4-(6-(3-methylisoxazol-4-yl)-1H-indol-3-yl)-N-(piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (S)-tert-butyl 3-((4-(6-(3-methylisoxazol-4-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (111 mg, 0.20 mmol) in DCM (6 mL) was added TFA (0.31 mL, 4.00 mmol), and the reaction mixture was stirred at RT for 1 h. The mixture was then concentrated and azeotroped for few times with DCM. The basified residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 0 to 100% gradient) to obtain the title compound as a white solid (49.6 mg, 0.11 mmol, 56% yield over 2 steps).

Example 5. Synthesis of 3,5-dimethyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)-pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole for Synthesis of Compound 116 Step 1: 3,5-dimethyl-4-(1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

To a solution of 6-bromo-1H-pyrrolo[2,3-b]pyridine (6.00 g, 30.5 mmol) in degassed 2:1 mixture of dioxane/water (150 mL) were added (3,5-dimethylisoxazol-4-yl)boronic acid (4.72 g, 33.5 mmol) and NaHCO₃ (5.12 g, 60.9 mmol), and the resulted suspension was degassed for 30 min. Pd(dppf)Cl₂ ([1,1′-Bis(diphenyl-phosphino)ferrocene]dichloropalladium(II)) DCM complex (620 mg, 0.76 mmol) was then added, and the reaction mixture was stirred at 100° C. for 2 h. After cooling down to RT, the mixture was extracted with EtOAc (3×30 mL), the combined organic phase was then washed with sat. aq. NaHCO₃ (2×20 mL) and brine (2×20 mL), dried over Na₂SO₄, filtered, and concentrated under reduced pressure to obtain the crude title compound as a tan solid (6.5 g, 30.5 mmol, quant. yield), which was used in the next step without further purification.

Step 2: 4-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

A suspension of 3,5-dimethyl-4-(1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (6.5 g, 30.5 mmol) in DCM (150 mL) was cooled to 0° C., and M amount of the required NBS (N-bromosuccinimide; 2.71 g, 15.2 mmol) was added portion wise followed by stirring for 30 min. Reaction was followed by LCMS (liquid chromatography mass spectrometry). After 30 min (where the conversion of about 40% was observed), the remaining % amount of NBS (2.71 g, 15.2 mmol) was added portion wise, and the reaction mixture was stirred for another 20 minutes. The reaction was then quenched by the addition of sat. aq. Na₂S₂O₃ and stirred vigorously for 16 h. After overnight, the mixture was concentrated under reduced pressure and re-dissolved in EtOAc (100 mL) and water (50 mL). Organic phase was separated, washed with sat. aq. NaHCO₃ (50 mL), water (2×50 mL), and brine (2×50 mL), then dried over Na₂SO₄, filtered, and concentrated under reduced pressure to provide the crude title compound as a brown solid (8.54 g, 29.2 mmol, 96% yield), which was used in the next step without further purification.

Step 3: 4-(3-bromo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

A solution of 4-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (8.54 g, 29.2 mmol) in dry THF (146 mL) at 0° C. was treated with NaOt-Bu (3.37 g, 35.1 mmol) and then was stirred for 30 min at this temperature before adding benzenesulfonyl chloride (3.92 mL, 30.7 mmol). The reaction mixture was then stirred for 30 min at 0° C. The mixture was concentrated to about 20 mL of THF remaining and diluted with water (70 mL). After sonication, the obtained suspension was filtered, the solid was rinsed with water and then dried for to provide the crude title compound as a red solid (12.64 g, 29.2 mmol, quant. yield), which was used in the next step without further purification.

Step 4: 3,5-dimethyl-4-(1-(phenylsulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

To a solution of 4-(3-bromo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (8.69 g, 20.1 mmol) in degassed dioxane (67 mL) were added bis(pinacolato)diboron (12.9 g, 50.7 mmol) and KOAc (9.91 g, 101.0 mmol), and the mixture was degassed for 30 min. Pd(dppf)Cl₂ DCM complex (1.63 g, 2.00 mmol) was added, and then the reaction mixture in the sealed tube was stirred at 100° C. for 1 h. The resulted black solution was cooled down to RT, diluted with EtOAc (100 mL), filtered through Celite and treated with sat. aq. NaHCO₃ (75 mL). Crude product was extracted with EtOAc (2×30 mL), combined organic phase was then washed with water (2×50 mL) and brine (2×50 mL), dried over Na₂SO₄, filtered, and concentrated under reduced pressure to a black sticky solid of crude title compound (9.61 g, 20.1 mmol, quant. yield), which was used in the next step without further purification.

Step 5: 3,5-dimethyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

To a solution of 3,5-dimethyl-4-(1-(phenylsulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (9.61 g, 20.1 mmol) in degassed 2:1 mixture of dioxane/water (100 mL) was added Cs₂CO₃ (13.06 g, 40.1 mmol), and obtained suspension was degassed for 30 min. 4-Chloro-2-(methylthio)-5-(trifluoromethyl)pyrimidine (US20130017194) (5.04 g, 22.1 mmol) and tetrakis(triphenylphosphine)palladium(0) (2.32 g, 2.01 mmol) were added, and the reaction mixture was stirred at 100° C. After 2 h, another portion of 4-chloro-2-(methylthio)-5-(trifluoromethyl)pyrimidine (1.00 g, 4.38 mmol) was added, and the reaction mixture was heated for another 30 min at 100° C. After cooling down to RT, the mixture was diluted with EtOAc (100 mL) and water (75 mL), and pH was adjusted to pH 8 with sat. aq. NaHCO₃. Crude product was extracted with EtOAc (3×75 mL), combined organic phase was then washed with water (2×50 mL) and brine (75 mL), separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient) to provide an orange paste, which was then re-purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 0 to 100% gradient) to give the title compound as a brown solid (2.05 g, 3.76 mmol, 19% yield).

Step 6: 3,5-dimethyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

To a solution of 3,5-dimethyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (2.00 g, 3.67 mmol) in DME (dimethoxyethane; 37 mL) was added m-CPBA (3-chloroperbenzoic acid; 77%) (1.65 g, 7.34 mmol), and the reaction mixture was stirred at RT for 2 h. The suspension was then filtered, and the solids were washed with DCM (20 mL) and EtOAc (20 mL). The collected organic filtrate was concentrated under reduced pressure, and the residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient). The title compound was obtained as a pale orange solid (1.08 g, 1.87 mmol, 51% yield).

Example 6. Synthesis of 4-(6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-N-((3R,4R)-4-methoxypiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 117) Step 1: Racemic trans tert-butyl 3-azido-4-methoxypiperidine-1-carboxylate

To a solution of racemic trans tert-butyl 3-azido-4-hydroxypiperidine-1-carboxylate (Angew. Chem., Int. Ed. 2016, 55, 11382) (504 mg, 2.08 mmol) in dry THF at 0° C. in an ice/water bath, was added sodium hydride (100 mg, 2.5 mmol) portion wise. The suspension was stirred at this temperature for 15 min. Then, iodomethane (0.144 mL, 2.29 mmol) was added. The resulting solution was allowed to reach RT and stirred for 16 h. After full conversion of starting material, the reaction mixture was quenched by addition of MeOH and then diluted with DCM. Water was added, and organic layer was separated, washed with brine (2×20 mL), dried over MgSO₄, filtered, and concentrated under reduced pressure. The yellowish residue was purified by silica gel chromatography (EtOAc in hexanes, 0 to 30% gradient). The title compound (511 mg, 1.99 mmol, 96% yield) was obtained as a translucent oil.

Step 2: Racemic trans tert-butyl 3-amino-4-methoxypiperidine-1-carboxylate

To a solution of racemic trans tert-butyl 3-azido-4-methoxypiperidine-1-carboxylate (511 mg, 1.99 mmol) in EtOH (ethanol; 10 mL) was added Pd/C, 10 wt. % (400 mg). The suspension was purged with hydrogen (three times). The resulting mixture was then stirred at RT for 3 h under atmospheric pressure of hydrogen. After full conversion of starting material, the suspension was filtered through a pad of Celite. The filtrate was concentrated under reduced pressure to provide the crude title compound as a yellowish oil, which was used in the next step without further purification.

Step 3: Racemic trans tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate

To a solution of 3,5-dimethyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (Example 5; 105 mg, 0.182 mmol) and racemic trans tert-butyl 3-amino-4-methoxypiperidine-1-carboxylate (63 mg, 0.273 mmol) in dry THF (0.9 mL) was added DIPEA (0.1 mL, 0.545 mmol). The reaction mixture was then stirred for 16 h at RT. The mixture was diluted with EtOAc (10 mL), washed with brine (2×10 mL). Organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The obtained crude title compound (130 mg, 0.179 mmol, 98% yield) was used in the next step without further purification.

Step 4: Racemic trans tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate

To a solution of racemic trans tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate (130 mg, 0.179 mmol) in dioxane (1.2 mL) was added 5M aq. NaOH (0.360 mL, 1.79 mmol). The reaction mixture was then stirred at room temperature for 16 h. After overnight, the mixture was concentrated under reduced pressure, and the residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 0 to 100% gradient). The title compound (65 mg, 0.111 mmol, 62% yield) was obtained as a pale yellow solid.

Step 5: (3R,4R)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate (A)

Racemic trans tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate (65 mg) was separated by chiral HPLC (high pressure liquid chromatography) using a ChiralPak IA column and 8:92 mixture of EtOH/Hexanes for elution. Two enantiomers were obtained: Peak 1 (A, tentatively assigned as (3R,4R), 20 mg, pale yellow solid), and Peak 2 (B, tentatively assigned as (3S,4S), 18 mg, pale yellow solid).

Step 6: 4-(6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-N-((3R,4R)-4-methoxypiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of Compound A from the previous step assigned as (3R,4R)-enantiomer (20 mg, 0.034 mmol) in DCM (1 mL) was added TFA (0.22 mL, 2.87 mmol). After 1 h of stirring at RT, reaction mixture was concentrated under reduced pressure, and the basified residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 10 to 50% gradient) to afford the title compound (9.4 mg, 0.019 mmol, 57% yield) as a white solid.

Example 7. Synthesis of 4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-N-((3R,4R)-4-methoxypiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 127) Step 1: (3R,4R)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate (A)

Racemic trans tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methoxypiperidine-1-carboxylate (Example 6; 197 mg, 0.271 mmol) was separated by chiral HPLC using a ChiralPak IA column and 8:20:72 mixture of MeOH/IPA/hexanes for elution. Two enantiomers were obtained: Peak 1 (A, tentatively assigned as (3R,4R), 84 mg, pale yellow solid), and Peak 2 (B, tentatively assigned as (3S,4S), 81 mg, pale yellow solid).

Step 2: 4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-N-((3R,4R)-4-methoxypiperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of Compound A from the previous step assigned as (3R,4R)-enantiomer (84 mg, 0.116 mmol) in dioxane (1 mL) was added 5M aq. NaOH (1.2 mL, 5.8 mmol). The reaction mixture was then stirred at 70° C. until full conversion. After 4 h, mixture was cooled down to RT and diluted in water. Aqueous layer was extracted with MeTHF (3×25 mL). Combined organic phase was washed with brine (50 mL), separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The obtained crude was re-dissolved in DCM (1.7 mL), and TFA (0.444 mL, 5.8 mmol) was added. After 1 h of stirring at RT, the reaction mixture was concentrated under reduced pressure, and the basified residue was purified by reverse phase chromatography (C18, MeCN in aq. 10 mM ammonium formate pH 3.8, 10 to 55% gradient) to afford the title compound (39.2 mg, 0.081 mmol, 70% yield over 2 steps) as a white solid.

Example 8. Synthesis of (S)-tert-butyl 3-((4-(6-(3-methylisothiazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate useful in the synthesis of Compound 128 Step 1: (S)-tert-butyl 3-((4-(1-(phenylsulfonyl)-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of (S)-tert-butyl 3-((4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (Example 3, step 1; 400 mg, 0.59 mmol) in degassed dioxane (4.2 mL) were added bis(pinacolato)diboron (373 mg, 1.47 mmol) and KOAc (288 mg, 2.95 mmol), and the mixture was degassed for 15 min. Pd(dppf)Cl₂ DCM complex (48 mg, 0.06 mmol) was added, and then the reaction mixture was stirred at 95° C. until full conversion (followed by LCMS). After 2 h, the mixture was cooled down to RT, diluted with EtOAc (50 mL), washed with sat. aq. NaHCO₃ (50 mL), water (50 mL), and brine (50 mL). Organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure to provide a brown semi-solid of crude title compound, which was used in the next step without further purification.

Step 2: (S)-tert-butyl 3-((4-(6-(3-methylisothiazol-4-yl)-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of (S)-tert-butyl 3-((4-(1-(phenylsulfonyl)-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (214 mg, 0.294 mmol) and 4-bromo-3-methylisothiazole (79 mg, 0.441 mmol) in previously degassed 2:1 mixture of dioxane/H₂O (6 mL) was added Na₂CO₃ (94 mg, 0.882 mmol), and the mixture was degassed for 15 min. Pd(dppf)Cl₂ DCM complex (24 mg, 0.029 mmol) was added, and the reaction mixture was stirred at 100° C. for 2 h. The mixture was cooled down to RT, diluted with EtOAc (30 mL), washed with sat. aq. NaHCO₃ (30 mL), water (30 mL), and brine (30 mL). The organic phase was separated, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (EtOAc in 1:1 mixture of hexanes/DCM, 0 to 100% gradient) to provide the title compound as a yellowish oil (152 mg, 74% yield).

Example 9. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 101) Step 1: 3,5-dimethyl-4-(1H-pyrrolo-[2,3-b]-pyridin-6-yl) isoxazole

A mixture of 6-bromo-1H-pyrrolo-[2,3-b]-pyridine (1 g, 5.08 mmol, 1 eq), (3,5-dimethylisoxazol-4-yl) boronic acid (1.43 g, 10.15 mmol, 2 eq), Pd(dppf)Cl₂.CH₂Cl₂ (207.23 mg, 253.77 μmol, 0.05 eq), NaHCO₃ (1.28 g, 15.23 mmol, 592.17 μL, 3 eq) in DME (10 mL) and H₂O (3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 12 h under N₂ atmosphere. The reaction mixture was poured into H₂O (20 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (20 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (1.1 g, 90% purity) as a white solid.

Step 2: 4-(3-bromo-1H-pyrrolo-[2,3-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole

To a solution of 3,5-dimethyl-4-(1H-pyrrolo-[2,3-b]-pyridin-6-yl) isoxazole (0.9 g, 4.22 mmol, 1 eq) in DMF (dimethylformamide; 10 mL) was added NBS (676.10 mg, 3.80 mmol, 0.9 eq). The mixture was stirred at 25° C. for 1 h. The reaction mixture was poured into H₂O (20 mL), and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (20 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (600 mg, crude) as pink solid which was used in the next step directly.

Step 3: 4-[1-(benzenesulfonyl)-3-bromo-pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole

To a solution of 4-(3-bromo-1H-pyrrolo[2,3-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole (0.6 g, 2.05 mmol, 1 eq) in DMF (9 mL) and THF (1 mL) was added NaH (98.58 mg, 2.46 mmol, 60% purity, 1.2 eq) and benzenesulfonyl chloride (471.58 mg, 2.67 mmol, 341.73 μL, 1.3 eq). The mixture was stirred at 25° C. for 1 h. The reaction mixture was poured into H₂O (20 mL) while white solid formed. The solid was filtered and concentrated under reduced pressure to afford the title compound (600 mg) as white solid, which used into the next step without further purification.

Step 4: 4-[1-(benzenesulfonyl) pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole; 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole

A mixture of 4-[1-(benzenesulfonyl)-3-bromo-pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole (0.27 g, 624.58 μmol, 1 eq), BPD (237.91 mg, 936.87 μmol, 1.5 eq), Pd(dppf)Cl₂ (45.70 mg, 62.46 μmol, 0.1 eq), KOAc (122.60 mg, 1.25 mmol, 2 eq) in dioxane (3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The reaction mixture was poured into H₂O (20 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (10 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (600 mg, crude, 2 Batches in parallel) as brown oil which was used into the next step without further purification.

Step 5: Tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

A mixture of 4-[1-(benzenesulfonyl) pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole and 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole (600 mg, from previous step), tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate ((PCT Int. Appl., WO2014124230); 476.63 mg, 1.25 mmol), Pd(dppf)Cl₂ (91.59 mg, 125.17 μmol), Na₂CO₃ (265.33 mg, 2.50 mmol) in dioxane (10 mL) and H₂O (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 12 h under N₂ atmosphere. The reaction mixture was poured into H₂O (30 mL) and extracted with EtOAc (30 mL×4). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (0.25 g, 286.65 μmol, 22.90% yield, 80% purity) as yellow solid.

Step 6: Tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (0.2 g, 286.65 μmol, 1 eq) in MeOH (1 mL) was added NaOH (2 M, 0.8 mL, 5.58 eq). The mixture was stirred at 60° C. for 1 h. The reaction mixture was concentrated under reduced pressure to afford the title compound (0.2 g, crude) as yellow solid, which was used into the next step without further purification.

Step 7: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (0.2 g, 358.70 μmol, 1 eq) in EtOAc (1 mL) was added HCl/EtOAc (4 M, 2 mL, 22.30 eq). The mixture was stirred at 25° C. for 1 h then concentrated under reduced pressure to give a residue that was purified by prep-HPLC (HCl condition) to afford the title compound (31.6 mg, HCl salt, 100% purity) as a yellow solid.

Example 10. Synthesis of 2-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo-[2,3-b]pyridin-6-yl]thiazole for use in Synthesizing Compound 108 Step 1: 1-(benzenesulfonyl)-6-bromo-pyrrolo[2,3-b]pyridine

To a solution of 6-bromo-1H-pyrrolo[2,3-b]pyridine (1 g, 5.08 mmol, 1 eq) in DMF (9 mL) and THF (1 mL) was added NaH (243.82 mg, 6.10 mmol, 60% purity, 1.2 eq) at 0° C. for 0.5 h, then benzenesulfonyl chloride (1.17 g, 6.60 mmol, 845.22 μL, 1.3 eq) was added to the solution at 0° C. The mixture was stirred at 20° C. for 12 h. The reaction mixture was diluted with water (100 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (30 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5/1) to afford the title compound (1.6 g, 4.27 mmol, 84.07% yield, 90% purity) as a white solid.

Step 2: 2-[1-(benzenesulfonyl)pyrrolo[2,3-b]pyridin-6-yl]thiazole

To a solution of 1-(benzenesulfonyl)-6-bromo-pyrrolo[2,3-b]pyridine (0.5 g, 1.48 mmol, 1 eq) in DMF (5 mL) was added tributyl (thiazol-2-yl) stannane (610.32 mg, 1.63 mmol, 1.1 eq), Pd(PPh₃)₄ (171.35 mg, 148.28 μmol, 0.1 eq) and CuI (28.24 mg, 148.28 μmol, 0.1 eq). The mixture was stirred at 130° C. for 12 h under N₂. The reaction mixture was diluted with saturated aqueous of KF (50 mL) and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (10 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=3/1) to afford the title compound (420 mg) as a white solid. (The reaction was combined with another reaction in 50 mg scale for purification.)

Step 3: 2-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]thiazole

To a solution of 2-[1-(benzenesulfonyl)pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.41 g, 1.20 mmol, 1 eq) in DMF (4 mL) was added NBS (213.74 mg, 1.20 mmol, 1 eq) at 0° C. The mixture was stirred at 20° C. for 12 h. The reaction mixture was diluted with water (50 mL) and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (10 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=6/1 to EtOAc) to afford the title compound (300 mg) as a pink red solid.

Step 4: 2-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo-[2,3-b]pyridin-6-yl]thiazole

To a solution of 2-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.8 g, 1.90 mmol, 1 eq) in dioxane (10 mL) was added BPD (725.01 mg, 2.86 mmol, 1.5 eq), KOAc (373.61 mg, 3.81 mmol, 2 eq) and Pd(dppf)Cl₂ (139.27 mg, 190.34 μmol, 0.1 eq). The mixture was stirred at 100° C. for 2 h under N₂. The reaction mixture was diluted with water (100 mL) 10 and extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (15 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (1 g) as a brown oil.

Example 11. Synthesis of Tert-butyl (5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl) pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,3-dimethyl-piperidine-1-carboxylate useful in the synthesis of Compound 115) Step 1: 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine

To a solution of 2,4-dichloro-5-(trifluoromethyl)pyrimidine (10 g, 46.09 mmol, 1 eq) in THF (200 mL) was added dropwise ZnCl₂ (1 M, 59.91 mL, 1.3 eq) at 0° C. After addition, the mixture was stirred at this temperature for 2 h, and then NaSMe (3.88 g, 55.31 mmol, 3.52 mL, 1.2 eq) was added dropwise at 0° C. The resulting mixture was stirred at 15° C. for 14 h. The mixture was quenched with aq. HCl (150 mL, 1M), and then extracted with EtOAc (60 mL×3), dried over Na₂SO₄ and concentrated. The residue was purified by column chromatography (SiO₂, PE/DCM=1:0 to 50:1) to afford the title compound (10 g, 43.74 mmol, 94.91% yield) as a colorless oil.

Step 2: 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo-[2,3-b]pyridin-6-yl]-3,5-dimethylisoxazole

To a solution of 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (Example 9; 3 g, 3.76 mmol, 1 eq) and 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (1.43 g, 5.63 mmol, 1.5 eq) in dioxane (30 mL)/H₂O (6 mL) was added Na₂CO₃ (1.19 g, 11.27 mmol, 3 eq) and Pd(dppf)Cl₂ (274.76 mg, 375.50 μmol, 0.1 eq). The mixture was stirred at 100° C. under N₂ atmosphere for 1 h. The reaction mixture was poured into water (150 mL). The aqueous phase was extracted with ethyl acetate (50 mL×3). The combined organic phase was washed with brine (50 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=10/1,4/1) to afford the title compound (0.7 g, 769.86 μmol, 20.50% yield, 60% purity) as a yellow solid.

Step 3: 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-pyrrolo[2,3-b]-pyridin-6-yl]-3,5-dimethylisoxazole

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (0.7 g, 1.28 mmol, 1 eq) in DCM (50 mL) was added m-CPBA (573.08 mg, 2.82 mmol, 2.2 eq). The mixture was stirred at 20° C. for 12 h. The residue was poured into a mixture of Sat.NaHCO₃ (20 mL) and Sat. Na₂SO₃ (20 mL), and the mixture was stirred for 5 min. The aqueous phase was extracted with DCM (30 mL×2). The combined organic phase was dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=10/1,2/1, contained 10% DCM) to afford the title compound (0.5 g, 822.43 μmol, 64.10% yield, 95% purity) as a white solid.

Step 4: Tert-butyl (5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,3-dimethyl-piperidine-1-carboxylate

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (0.1 g, 173.14 μmol, 1 eq), tert-butyl (5S)-5-amino-3,3-dimethyl-piperidine-1-carboxylate (114.01 mg, 207.77 μmol, 1.2 eq, FA) in THF (3 mL) was added DIEA (111.89 mg, 865.72 μmol, 150.79 μL, 5 eq). The mixture was stirred at 20° C. under N₂ atmosphere for 1 h. The reaction mixture was poured into water (30 mL). The aqueous phase was extracted with EtOAc (20 mL×3). The combined organic phase was washed with brine (20 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=10/1,2/1) to afford the title compound (0.12 g) as yellow solid.

Example 12. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo-[3,4-b]-pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 118) Step 1: 3,5-dimethyl-4-(1H-pyrazolo-[3,4-b]-pyridin-6-yl) isoxazole

A mixture of 6-chloro-1H-pyrazolo-[3,4-b]-pyridine (1 g, 6.51 mmol, 1 eq), (3,5-dimethylisoxazol-4-yl) boronic acid (1.38 g, 9.77 mmol, 1.5 eq), Pd(dppf)Cl₂.CH₂Cl₂ (531.77 mg, 651.17 μmol, 0.1 eq), K₂CO₃ (5 M, 3.91 mL, 3 eq) in dioxane (20 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. The reaction mixture was poured into water (100 mL), and then extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (200 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (1 g) as a yellow solid.

Step 2: 4-(3-iodo-1H-pyrazolo-[3,4-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole

To a solution of 3,5-dimethyl-4-(1H-pyrazolo-[3,4-b]-pyridin-6-yl) isoxazole (0.9 g, 4.20 mmol, 1 eq) in DMF (10 mL) was added KOH (942.92 mg, 16.80 mmol, 4 eq) and molecular iodine (2.13 g, 8.40 mmol, 1.69 mL, 2 eq). The mixture was stirred at 140° C. for 3 h. The reaction mixture was quenched by addition 10% Na₂SO₃ (100 mL) at 15° C., then extracted with EtOAc (50 mL×3), dried over Na₂SO₄ and concentrated to afford the title compound (1 g, crude) as a yellow solid.

Step 3: 4-(3-iodo-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole

To a solution of 4-(3-iodo-1H-pyrazolo-[3,4-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole (0.9 g, 2.65 mmol, 1 eq) in DCM (1 mL) was added 3,4-dihydro-2H-pyran (267.10 mg, 3.18 mmol, 290.32 μL, 1.2 eq) and PTSA (p-toluenesulfonic acid; 45.57 mg, 264.61 μmol, 0.1 eq). The mixture was stirred at 25° C. for 3 h. The mixture was washed with Sat.NaHCO₃ (100 mL×2) and brine (200 mL), dried over Na₂SO₄, filtered and the filtrate was evaporated. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (0.8 g, 90% purity) as a white solid.

Step 4: 3,5-dimethyl-4-[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl]-isoxazole

A mixture of 4-(3-iodo-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl)-3,5-dimethyl-isoxazole (0.25 g, 589.30 μmol, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (134.73 mg, 589.30 μmol, 1 eq), Pd(PPh₃)₄ (68.10 mg, 58.93 μmol, 0.1 eq), trimethyl (trimethylstannyl) stannane (193.07 mg, 589.30 μmol, 122.20 μL, 1 eq) in Tol. (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 16 h under N₂ atmosphere. The reaction mixture was poured into aq. KF (50 mL), and then extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (100 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 3/1) to afford the title compound (150 mg, 305.81 μmol, 51.89% yield) as a yellow solid.

Step 5: 3,5-dimethyl-4-[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl]-isoxazole

To a solution of 3,5-dimethyl-4-[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl]-isoxazole (0.15 g, 305.81 μmol, 1 eq) in DCM (1 mL) was added m-CPBA (155.22 mg, 764.53 μmol, 85% purity, 2.5 eq). The mixture was stirred at 15° C. for 16 h. The reaction mixture was quenched by addition Sat.Na₂SO₃ (5 mL) and NaHCO₃ (5 mL), stirred at this temperature for 10 min and then extracted with DCM (10 mL×2). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was triturated with PE:EtOAc (5:1.5 mL). The solid was filtered and dried to afford the title compound (100 mg, 191.39 μmol, 62.58% yield) as a yellow solid.

Step 6: Tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

A mixture of 3,5-dimethyl-4-[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-6-yl]-isoxazole (0.1 g, 191.39 μmol, 1 eq), tert-butyl (3S)-3-aminopiperidine-1-carboxylate (57.50 mg, 287.08 μmol, 1.5 eq), DIEA (74.20 mg, 574.16 μmol, 100.01 μL, 3 eq) in THF (1 mL) was as stirred at 15° C. for 3 h. It was concentrated. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (100 mg) as a yellow gum.

Step 7: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo-[3,4-b]-pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo-[3,4-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (0.06 g, 93.36 μmol, 1 eq) in DCM (1 mL) was added Et₃SiH (32.57 mg, 280.08 μmol, 44.73 μL, 3 eq) and TFA (212.90 mg, 1.87 mmol, 138.25 μL, 20 eq). The mixture was stirred at 20° C. for 5 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (HCl condition) to afford the title compound (20.4 mg, HCl salt, 100% purity) as a yellow solid.

Example 13. Synthesis of (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-N,N-dimethyl-piperidine-3-carboxamide (Compound 119) Step 1: O1-tert-butyl-O3-methyl(3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1,3-dicarboxylate

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-pyrrolo[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (Example 11; 260 mg, 450.17 μmol, 1 eq) in THF (5 mL) was added DIPEA (290.91 mg, 2.25 mmol, 392.06 μL, 5 eq) and O1-tert-butyl O3-methyl (3R,5S)-5-aminopiperidine-1,3-dicarboxylate (174.43 mg, 675.26 μmol, 1.5 eq). The mixture was stirred at 15° C. for 1 h. The reaction mixture was diluted with H₂O (15 mL), and then extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (40 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10:1 to 1:1) to afford the title compound (240 mg) as a yellow solid.

Step 2: (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxylic acid

To a solution of O1-tert-butyl-O3-methyl(3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1,3-dicarboxylate (220 mg, 291.10 μmol, 1 eq) in MeOH (2 mL) was added NaOH (2 M, 2.00 mL, 13.74 eq). The mixture was stirred at 15° C. for 1 h. The reaction mixture was concentrated under reduced pressure to remove MeOH. The residue was diluted with H₂O (15 mL) and acidified by 2N HCl to pH=2 and extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (140 mg) as a yellow solid.

Step 3: tert-butyl(3R,5S)-3-(dimethylcarbamoyl)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxylic acid (60 mg, 99.74 μmol, 1 eq) in THF (1 mL) was added T₃P (190.41 mg, 299.21 μmol, 177.95 μL, 50% purity, 3 eq), DIPEA (64.45 mg, 498.69 μmol, 86.86 μL, 5 eq) and N-methylmethanamine (2 M, 249.35 μL, 5 eq). The mixture was stirred at 15° C. for 12 h. The reaction mixture was diluted with H₂O (15 mL), and then extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (40 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (50 mg) as yellow solid.

Step 4: (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-N,N-dimethyl-piperidine-3-carboxamide

To a solution of tert-butyl(3R,5S)-3-(dimethylcarbamoyl)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (40 mg, 63.63 μmol, 1 eq) was added HCl/EtOAc (4 M, 2 mL). The mixture was stirred at 15° C. for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC to afford the title compound (13.4 mg, FA) as white solid.

Example 14. Synthesis of Tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-(methylcarbamoyl)piperidine-1-carboxylate useful in the synthesis of Compound 120

To a solution of (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxylic acid (60 mg, 99.74 μmol, 1 eq) in THF (1 mL) was added T₃P (190.41 mg, 299.21 μmol, 177.95 μL, 50% purity, 3 eq), DIPEA (64.45 mg, 498.69 μmol, 86.86 μL, 5 eq) and methanamine (2M, 249.35 μL, 5 eq). The mixture was stirred at 15° C. for 12 h. The reaction mixture was diluted with H₂O (10 mL) and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (20 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=1:1 to 1:20) to afford the title compound (50 mg) as white solid.

Example 15. Synthesis of (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-N, N-dimethyl-piperidine-3-carboxamide (Compound 112) Step 1: 2-[[6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-indol-1-yl]-methoxy]-ethyl-trimethyl-silane

To a solution of 6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole (Example 19, step 1; 2 g, 5.31 mmol, 1 eq) in THF (20 mL) was added NaH (254.94 mg, 6.37 mmol, 60% 25 purity, 1.2 eq) at −10° C. After addition, the mixture was stirred at this temperature for 30 min, and then 2-(chloromethoxy) ethyl-trimethyl-silane (1.33 g, 7.97 mmol, 1.41 mL, 1.5 eq) was added dropwise at −10° C. The resulting mixture was stirred at 0° C. for 1 h. The reaction mixture was diluted with water (150 mL) and extracted with ethyl acetate (80 mL×2). The combined organic layers were washed with brine (200 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=50:1 to 20:1) to afford the title compound (2.6 g) as a white solid.

Step 2: O1-tert-butyl-O3-methyl-(3R,5S)-5-[[4-[6-bromo-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1,3-dicarboxylate

A mixture of 2-[[6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-indol-1-yl]-methoxy]-ethyl-trimethyl-silane (1.46 g, 2.87 mmol, 1 eq), O1-tert-butyl-O3-methyl-(3R,5S)-5-aminopiperidine-1,3-dicarboxylate (0.89 g, 3.45 mmol, 1.2 eq) and DIEA (1.11 g, 8.61 mmol, 1.50 mL, 3 eq) in NMP (15 mL) was stirred at 140° C. for 1 h. The reaction mixture was diluted with water (100 mL) and extracted with EtOAc (50 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO2, PE/EtOAc=30:1 to 5:1) to afford the title compound (1.68 g, 2.21 mmol, 77.09% yield, 96% purity) as a white solid.

Step 3: O1-tert-butyl-O3-methyl-(3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1,3-dicarboxylate

A mixture of O1-tert-butyl-O3-methyl-(3R,5S)-5-[[4-[6-bromo-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1,3-dicarboxylate (0.7 g, 960.65 μmol, 1 eq), (3,5-dimethylisoxazol-4-yl)boronic acid (270.77 mg, 1.92 mmol, 2 eq), Pd(dppf)Cl₂.CH₂Cl₂ (78.45 mg, 96.07 μmol, 0.1 eq) and NaHCO₃ (242.11 mg, 2.88 mmol, 112.09 μL, 3 eq) in DME (9 mL), H₂O (3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The reaction mixture was diluted with water (100 mL) and extracted with EtOAc (50 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10:1 to 5:1) to afford the title compound (600 mg) as a yellow solid.

Step 4: (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-3-carboxylic acid

To a solution of O1-tert-butyl-O3-methyl-(3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1,3-dicarboxylate (550 mg, 738.38 μmol, 1 eq) in MeOH (6 mL) was added NaOH (2 M, 3.69 mL, 10 eq). The mixture was stirred at 20° C. for 0.5 h. The reaction mixture was adjusted pH to 4 with aqueous HCl (0.5 M, 80 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (90 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue to afford the title compound (600 mg, crude) was used into the next step without further purification.

Step 5: Tert-butyl (3R,5S)-3-(dimethylcarbamoyl)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-ylamino]-piperidine-1-carboxylate

To a solution of (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-3-carboxylic acid (0.2 g, 273.65 μmol, 1 eq) in THF (2 mL) was added T₃P (1.74 g, 2.74 mmol, 1.63 mL, 50% purity, 10 eq) and DIEA (530.51 mg, 4.10 mmol, 714.97 μL, 15 eq), N-methylmethanamine (2 M, 2.74 mL, 20 eq). The mixture was stirred at 20° C. for 1 h. The reaction mixture was diluted with water (100 mL) and extracted with EtOAc (50 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5:1 to 1:1) to afford the title compound (200 mg) as a colorless oil.

Step 6: (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-N, N-dimethyl-piperidine-3-carboxamide

To a solution of tert-butyl (3R,5S)-3-(dimethylcarbamoyl)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (0.18 g, 237.49 μmol, 1 eq) in dioxane (2 mL) was added H₂SO₄ (232.93 mg, 2.37 mmol, 126.59 μL, 10 eq). The mixture was stirred at 40° C. for 2 h. The mixture was adjusted pH to 8 with saturated aqueous K₂CO₃ and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (HCl condition) to afford the title compound (28.6 mg, HCl salt) as a yellow solid.

Example 16. Synthesis of Tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-5-(methylcarbamoyl) piperidine-1-carboxylate useful in the synthesis of Compound 113

To a solution of (3R,5S)-1-tert-butoxycarbonyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-3-carboxylic acid (0.2 g, 273.65 μmol, 1 eq) in THF (5 mL) was added T₃P (1.74 g, 2.74 mmol, 1.63 mL, 50% purity, 10 eq) and DIEA (530.51 mg, 4.10 mmol, 714.97 μL, 15 eq), methanamine (2 M, 2.74 mL, 20 eq). The mixture was stirred at 20° C. for 1 h. The reaction mixture was diluted with water (100 mL) and extracted with ethyl acetate (50 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=5:1 to 1:1) to afford the title compound (200 mg) as a white solid.

Example 17. Synthesis of Tert-butyl(5S)-3,3-dimethyl-5-[[4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate useful in the Synthesis of Compound 109 Step 1: N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-[6-bromo-1-(2-trimethylsilylethoxy methyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

A mixture of 2-[[6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]indol-1-yl]methoxy ethyl-trimethyl-silane (270 mg, 532.74 μmol, 1 eq), (3S)-1-benzyl-5,5-dimethyl-piperidin-3-amine (135.74 mg, 532.74 μmol, 1 eq, HCl) and DIEA (344.26 mg, 2.66 mmol, 463.96 μL, 5 eq) in NMP (2.7 mL) was heated to 75° C. and stirred for 6 h. The mixture was poured into water 20 mL, and extracted with EtOAc (20 mL×3). The combined organic layer was washed with brine (50 mL), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by MPLC (SiO₂, PE/EtOAc=10/1 to 1:1) to afford the title compound (230 mg, 91.5% purity) as yellow oil.

Step 2N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a mixture of N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-[6-bromo-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (200 mg, 290.40 μmol, 1 eq) in DMF (0.5 mL) was added tributyl(thiazol-2-yl)stannane (325.98 mg, 871.21 μmol, 3 eq), CuI (5.53 mg, 29.04 μmol, 0.1 eq) and Pd(PPh₃)₄ (33.56 mg, 29.04 μmol, 0.1 eq). The mixture was heated to 130° C. and stirred for 12 h under N₂. Saturated KF solution (20 mL) was added and the reaction mixture was stirred for about 1 hr. Then the reaction mixture was extracted by EtOAc (20 mL×3). The organic layer was combined, washed by brine (100 mL), dried over Na₂SO₄, filtered and evaporated to afford the residue. The residue was purified by MPLC (SiO₂, PE/EtOAc=10/1 to 1:1) to afford the title compound (125 mg, 85.2% purity) as yellow solid.

Step 3: tert-butyl(5S)-3,3-dimethyl-5-[[4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a mixture of N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (95 mg, 137.10 μmol, 1 eq) and Boc₂O (di-t-butyl dicarbonate; 149.61 mg, 685.51 μmol, 157.49 μL, 5 eq) in THF (1 mL) was added Pd/C (15 mg, 10% purity) under N₂. The suspension was degassed under vacuum and purged with H₂ several times. The mixture was stirred for 34 h at 25° C. under H₂ (15 psi). The mixture was filtered, and the filtrate was concentrated to afford the title compound (200 mg, crude, 73.4% purity) as brown oil.

Example 18. Synthesis of (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (Compound 105) Step 1: tert-butyl N-[(3S,5R)-1-benzyl-5-hydroxy-3-piperidyl]carbamate

To a solution of tert-butyl N-[(3S,5R)-1-benzyl-5-[tert-butyl(dimethyl)silyl]oxy-3-piperidyl]carbamate (8.6 g, 20.44 mmol, 1 eq) in THF (50 mL) was added TBAF (1 M, 22.49 mL, 1.1 eq). The reaction mixture was stirred at 30° C. for 12 h. The reaction mixture was evaporated to afford a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=3/1) to afford the title compound (5.4 g, 17.45 mmol, 85.34% yield, 99% purity) as white solid.

Step 2: (3R,5S)-5-amino-1-benzyl-piperidin-3-ol

Tert-butyl N-[(3S,5R)-1-benzyl-5-hydroxy-3-piperidyl]carbamate (5.4 g, 17.62 mmol, 1 eq) dissolved in HCl/EtOAc (25 mL) was stirred at 30° C. for 1 h under N₂ atmosphere. The reaction mixture was evaporated to afford the product to afford the title compound (4.2 g, 16.61 mmol, 94.25% yield, 96% purity, HCl salt) as pink solid. It will be used directly in next step.

Step 3: (3R,5S)-1-benzyl-5-[[4-(6-bromo-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

A flask was fitted with 6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole (Example 19; 500 mg, 1.33 mmol, 1 eq), (3R,5S)-5-amino-1-benzyl-piperidin-3-ol (322.32 mg, 1.33 mmol, 1 eq, HCl) and DIPEA (858.05 mg, 6.64 mmol, 1.16 mL, 5 eq) in NMP (1 mL). The reaction mixture was heated to 70° C. for 12 h. The combined mixture was poured into H₂O (50 mL). EtOAc (40 mL×3) was used to extract the product. The organic layer was washed by brine (30 mL), dried over Na₂SO₄, filtered and evaporated to afford the crude product. The crude product was purified by MPLC (SiO₂, PE/EtOAc=3/1-1/1) to afford the title compound (1 g, 32.6% purity) as light yellow oil.

Step 4: (3R,5S)-1-benzyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

(3R,5S)-1-benzyl-5-[[4-(6-bromo-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (700 mg, 1.28 mmol, 1 eq), (3,5-dimethylisoxazol-4-yl)boronic acid (361.11 mg, 2.56 mmol, 2 eq), Pd(PPh₃)₄ (296.09 mg, 256.23 μmol, 0.2 eq) and Na₂CO₃ (271.58 mg, 2.56 mmol, 2 eq) in DMF (10 mL) and H₂O (2 mL) was de-gassed and then heated to 130° C. for 12 h under N₂. The combined reaction mixture was poured into H₂O (40 mL). EtOAc (40 mL×3) was used to extract the product. The organic layer was washed by brine (30 mL), dried over Na₂SO₄, filtered and evaporated to afford the crude product. The crude product was purified by MPLC (SiO₂, PE/EtOAc=1/1) to afford the title compound (460 mg, 44.2% purity) as yellow solid. It contains some TPPO.

Step 5: tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxypiperidine-carboxylate

To a solution of (3R,5S)-1-benzyl-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (360 mg, 639.90 μmol, 1 eq) and Boc₂O (279.31 mg, 1.28 mmol, 294.01 μL, 2 eq) in THF (10 mL) was added Pd/C (120 mg, 10% purity) under N₂. The suspension was degassed under vacuum and purged with H₂ several times. The mixture was stirred under H₂ (15 psi) at 30° C. for 8.5 h. The reaction mixture was filtered through celite and the cake was washed by THF (15 mL). The filtrate was evaporated to afford the title compound (400 mg, crude) as yellow oil. It contains some TPPO and was used directly in next step without any further purification.

Step 6: (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

A mixture of tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate (400 mg, 698.60 μmol, 1 eq) in HCl/EtOAc (15 mL) was stirred at 30° C. for 1 h. The reaction mixture was evaporated to afford a residue. Then H₂O (10 mL) was added to the mixture and PE/EtOAc (10/1, 15 mL×3) was used to extract undesired TPPO. The aqueous was evaporated to afford the crude product. The combined crude product was purified by acidic prep-HPLC (HCl condition). The separated solution was lyophilized after removing MeCN to afford the title compound (53.3 mg, 99.7% purity, HCl salt) as yellow solid.

Example 19. Synthesis of N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-(6-bromo-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine useful in the synthesis of Compound 102) Step 1: 6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole

To a solution of 2,4-dichloro-5-(trifluoromethyl)pyrimidine (22.58 g, 104.06 mmol, 1.2 eq) in DCE (1,2-dichloroethane; 200 mL) was added AlCl₃ (15.03 g, 112.73 mmol, 6.16 mL, 1.3 eq). The mixture was stirred at 80° C. for 0.5 h. Then 6-bromo-1H-indole (17 g, 86.72 mmol, 1 eq) was added to the solution at 80° C. The mixture was stirred at 80° C. for 11.5 h. The reaction mixture was diluted with water (1500 mL) and extracted with EtOAc (500 mL×3). The combined organic layers were washed with brine (200 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 3/1), then the residue was washed with MeOH (200 mL), filtered to afford the title compound (9.9 g, 26.29 mmol, 30.32% yield, 100% purity) as white solid.

Step 2: N-[(3S)-1-benzyl-5,5-dimethyl-3-piperidyl]-4-(6-bromo-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

A mixture of (3S)-1-benzyl-5,5-dimethyl-piperidin-3-amine (676.65 mg, 2.66 mmol, 1 eq, HCl), 6-bromo-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole (1 g, 2.66 mmol, 1 eq) and DIEA (1.72 g, 13.28 mmol, 2.31 mL, 5 eq) in NMP (3 mL) was heated to 75° C. and stirred for 3 h under N₂. The mixture was poured into water 20 mL, and extracted with EtOAc (20 mL×3). The combined organic layer was washed with brine (50 mL), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by MPLC (SiO₂, PE/EtOAc=7/1, 1500 mL) to afford the title compound as yellow solid.

Example 20. Synthesis of (3R,5S)-1-benzyl-5-[[4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidin-3-ol Useful in the Synthesis of Compound 107)

A mixture of (3R,5S)-1-benzyl-5-[[4-[6-bromo-1-(2-trimethylsilylethoxymethyl) indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidin-3-ol (400 mg, 591.16 μmol, 1 eq), tributyl (thiazol-2-yl) stannane (663.58 mg, 1.77 mmol, 3 eq), CuI (11.26 mg, 59.12 μmol, 0.1 eq), Pd(PPh₃)₄ (68.31 mg, 59.12 μmol, 0.1 eq) and in DMF (5 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 130° C. for 16 h under N₂ atmosphere. The reaction mixture was quenched by addition saturated CsF solution (20 mL), extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine 20 mL, dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5/1 to 4/1) to afford the title compound (328 mg) as a yellow solid.

Example 21. Synthesis of 4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-indol-3-yl]-N-[(3S)-3-piperidyl]-5 (trifluoromethyl)pyrimidin-2-amine (Compound 121) Step 1: Methyl 3-[2-chloro-5-(trifluoromethyl) pyrimidin-4-yl]-1H-indole-6-carboxylate

To a solution of 2, 4-dichloro-5-(trifluoromethyl) pyrimidine (24.77 g, 114.16 mmol, 2.00 eq) in DCE (200.00 mL) was added AlCl₃ (15.98 g, 119.87 mmol, 6.55 mL, 2.10 eq). The mixture was stirred at 90° C. for 30 min, and then methyl 1H-indole-6-carboxylate (10.00 g, 57.08 mmol, 1.00 eq) was added at 90° C. The resulting mixture was stirred at 90° C. for 15.5 h. The reaction mixture was filtered. The filtrate was diluted with water (200 mL) and extracted with DCM (80 mL×3). The combined organic layers were washed with brine (200 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was washed with MeOH (50 mL) and filtered to afford the title compound (4.00 g, 10.57 mmol, 18.52% yield, 94% purity) as a yellow solid.

Step 2: Methyl 3-[2-[[(3S)-1-tert-butoxycarbonyl-3-piperidyl] amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carboxylate

A mixture of methyl 3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carboxylate (2.50 g, 7.03 mmol, 1.00 eq), tert-butyl (3S)-3-aminopiperidine-1-carboxylate (1.83 g, 9.14 mmol, 1.30 eq), DIEA (4.54 g, 35.15 mmol, 6.14 mL, 5.00 eq) in NMP (10.00 mL) was stirred at 140° C. for 1 h. The reaction mixture was poured into water 200 mL, and then extracted with EtOAc (70 mL×3). The combined organic layers were washed with brine (300 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5:1 to 1:1) to afford the title compound (2.20 g, 3.39 mmol, 48.19% yield, 80% purity) as a yellow solid.

Step 3: 3-[2-[[(3S)-1-tert-butoxycarbonyl-3-piperidyl] amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carboxylic acid

A mixture of methyl 3-[2-[[(3S)-1-tert-butoxycarbonyl-3-piperidyl] amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carboxylate (2.20 g, 4.23 mmol, 1.00 eq), LiOH (5 M, 1.69 mL, 2.00 eq) in MeOH (20.00 mL) was stirred at 25° C. for 3 h. The reaction mixture was concentrated, and then diluted with water 100 mL and extracted with EtOAc (50 mL×3). The organic layers was removed, and the aqueous phase was adjusted pH to 1 by HCl (1M), extracted with EtOAc (50 mL×3). The combined organic layers were washed with brine (300 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (1.80 g, 3.20 mmol, 75.57% yield, 90% purity) as a yellow solid.

Step 4: Tert-butyl (3S)-3-[[4-[6-[[(Z)—N-hydroxy-C-methyl-carbonimidoyl]-carbamoyl]-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

A mixture of 3-[2-[[(3S)-1-tert-butoxycarbonyl-3-piperidyl]-amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carboxylic acid (200 mg, 395.66 μmol, 1 eq), N-hydroxyacetamidine (58.62 mg, 791.31 μmol, 2 eq), HOBt (1-hydroxybenzotriazole; 106.92 mg, 791.31 μmol, 2 eq), EDCI (151.70 mg, 791.31 μmol, 2 eq) and DIPEA (255.68 mg, 1.98 mmol, 344.58 μL, 5 eq) in acetonitrile (ACN; 9 mL). The mixture was stirred at 30° C. for 7 h. The reaction mixture was concentrated under reduced pressure to afford the title compound (240 mg, crude) as white solid. The crude product was used directly into the next step without purification.

Step 5: Tert-butyl (3S)-3-[[4-[6-(3-methyl-1, 2,4-oxadiazol-5-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

A solution of tert-butyl (3S)-3-[[4-[6-[[(Z)—N-hydroxy-C-methyl-carbonimidoyl]-carbamoyl]-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (240 mg, 427.38 μmol, 1 eq) in Diglyme (10 mL) was stirred at 100° C. for 12 h. The reaction mixture was concentrated under reduced pressure to remove digylme. The residue was diluted with H₂O (50 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (60 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5/1 to 1/1) to afford the title compound (100 mg) as yellow solid.

(The reaction was combined with another reaction in 70 mg scale for purification and work up.)

Step 6: 4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-indol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A solution of tert-butyl (3S)-3-[[4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (80 mg, 147.18 μmol, 1 eq) in HCl/EtOAc (4 M, 8.00 mL, 217.42 eq) was stirred at 15° C. for 30 min. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (FA condition) to afford the title compound (64 mg, FA, 100% purity) as white solid.

(The reaction was combined with another reaction in 20 mg scale for purification and work-up.)

Example 22. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indazol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 100) Step 1: Tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxy methyl) indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

A mixture of tert-butyl (3S)-3-[[4-[6-bromo-1-(2-trimethylsilylethoxymethyl)indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.3 g, 446.68 μmol, 1 eq), (3,5-dimethylisoxazol-4-yl)boronic acid (75.54 mg, 536.02 μmol, 1.2 eq), Pd(PPh₃)₄ (51.62 mg, 44.67 μmol, 0.1 eq) and Na₂CO₃ (94.69 mg, 893.36 μmol, 2 eq) in DMF (20 mL), H₂O (4 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 130° C. for 2 h under N₂ atmosphere. The reaction mixture was diluted with water (50 mL) and extracted with EtOAc (20 ml×3). The combined organic layers were washed with brine (50 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10:1 to 5:1) to afford the title compound (260 mg) as a yellow oil.

(The reaction was combined with another reaction in 50 mg scale for purification.)

Step 2: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-indazol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-(2-trimethylsilylethoxymethyl) indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (210 mg, 305.31 μmol, 1 eq) in dioxane (4 mL) was added H₂SO₄ (299.45 mg, 3.05 mmol, 162.74 μL, 10 eq). The mixture was stirred at 40° C. for 2 h. The reaction mixture was adjusted pH to 8 with saturated aqueous Na₂CO₃ and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (FA condition) to afford the title compound (49.4 mg, FA, purity 98.479%) as a white solid.

Example 23. Synthesis of Tert-butyl (3S)-3-[[4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl) indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate useful in the Synthesis of Compound 103 Step 1: Tert-butyl(3S)-3-[[4-[6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-(2-trimethylsilylethoxymethyl)indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of tert-butyl (3S)-3-[[4-[6-bromo-1-(2-trimethylsilylethoxymethyl)indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (400 mg, 595.57 μmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (302.48 mg, 1.19 mmol, 2 eq), Pd(dppf)Cl₂ (43.58 mg, 59.56 μmol, 0.1 eq) and AcOK (175.35 mg, 1.79 mmol, 3 eq) in DME (4 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 2 h under N₂ atmosphere. The reaction mixture was diluted with water 40 mL and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (80 mL×1), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=20:1 to 10:1) to afford the title compound (400 mg) as a yellow oil.

Step 2: Tert-butyl (3S)-3-[[4-[6-thiazol-2-yl-1-(2-trimethylsilylethoxymethyl) indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of tert-butyl (3S)-3-[[4-[6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-(2-trimethylsilylethoxymethyl)indazol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (350 mg, 487.00 μmol, 1 eq), 2-bromothiazole (103.84 mg, 633.10 μmol, 57.06 μL, 1.3 eq), Pd(dppf)Cl₂ (35.63 mg, 48.70 μmol, 0.1 eq) and Na₂CO₃ (51.62 mg, 487.00 μmol, 1 eq) in dioxane (5 mL), H₂O (1 mL) as degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 2 h under N₂ atmosphere. The reaction mixture was diluted with water 20 mL and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10:1 to 2:1) to give a residue. The residue was purified again by prep-TLC (thin layer chromatography; SiO₂, PE:EtOAc=3:1) to afford the title compound (160 mg) as a yellow solid.

Example 24. Synthesis of 4-[6-(1-methyltetrazol-5-yl)-1Hindol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 122) Step 1: 5-bromo-1-methyl-tetrazole

A suspension of 1-methyltetrazole-5-thiol (0.5 g, 4.30 mmol, 1 eq), ZnBr₂ (1.94 g, 8.61 mmol, 430.88 μL, 2 eq) in AcOH (10 mL) was heated to 40° C. for 0.5 h, then peroxyacetic acid (13.10 g, 25.83 mmol, 11.39 mL, 6 eq) was added to the above carefully and the resulting mixture was stirred at 80° C. for 11.5 h. The reaction mixture was cooled to 15° C. and poured into ice-water (1000 mL) and adjusted pH to 9 with NaHCO₃ (50 g). The aqueous phase was extracted with EtOAc (200 mL×3). The combined organic phase was washed with Sat. Na₂SO₃ (500 mL×2). The combined organic phase was dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (0.45 g, crude) as white solid and used directly.

Step 2: Tert-butyl (3S)-3-[[4-[6-(1-methyltetrazol-5-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate

To a solution of (S)-tert-butyl 3-((4-(1-(phenylsulfonyl)-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (Example 8; 0.1 g, 137.44 μmol, 1 eq), 5-bromo-1-methyl-tetrazole (33.60 mg, 206.16 μmol, 1.5 eq) in dioxane (2 mL)/H₂O (0.4 mL) was added Pd(dppf)Cl₂ (10.06 mg, 13.74 μmol, 0.1 eq) and Na₂CO₃ (43.70 mg, 412.31 μmol, 3 eq). The mixture was stirred at 100° C. under N₂ atmosphere for 12 h. The reaction mixture was cooled to 15° C. and poured into water (20 mL). The aqueous phase was extracted with EtOAc (20 mL×3). The combined organic phase was dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=5/1, 1/1) to afford the title compound (40 mg, 58.87 μmol, 42.84% yield, 80% purity) as yellow solid.

Step 3: 4-[6-(1-methyltetrazol-5-yl)-1Hindol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A solution of tert-butyl (3S)-3-[[4-[6-(1-methyltetrazol-5-yl)-1H-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-piperidine-1-carboxylate (40 mg, 73.59 μmol, 1 eq) in HCl/EtOAc (10 mL) was stirred at 15° C. for 1 h. The reaction mixture was concentrated in vacuum. The residue was purified by twice prep-HPLC (HCl condition) to afford the title compound (9 mg, HCl salt 99% purity) as a yellow solid. The reaction was combined with another reaction in 30 mg scale for purification.

Example 25. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 124) and 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 125) Step 1: 4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl) pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-ol

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-pyrrolo[2,3-b]-pyridin-6-yl]-3,5-dimethyl-isoxazole (Example 11; 1.9 g, 2.44 mmol, 1 eq) in DCM (50 mL) was added m-CPBA (1.16 g, 5.36 mmol, 2.2 eq). The mixture was stirred at 20° C. for 12 h. The residue was poured into a mixture of Sat.NaHCO₃ (20 mL) and Sat. Na₂SO₃ (20 mL), and the mixture was stirred for 5 min. The aqueous phase was extracted with DCM (30 mL×2). The combined organic phase was dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was washed with a mixture of PE:EtOAc=5:1 (20 mL), filtered and the filter cake was collected to afford the title compound (1 g, crude) as yellow solid and used directly.

Step 2: 4-[1-(benzenesulfonyl)-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-pyrrolo-[2,3-b]-pyridin-6-yl]-3,5-dimethylisoxazle

A solution of 4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl) pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-ol (1 g, 1.94 mmol, 1 eq) in POCl₃ (15 mL) was stirred at 90° C. for 0.5 h. The solution was cooled to 15° C. and concentrated in vacuum. The residue was adjusted pH to 9 with sat. NaHCO₃ and extracted with ethyl acetate (50 mL×3). The combined organic phase was dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (0.6 g, crude) as a yellow solid and used directly.

Step 3: Benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate and Benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 4-[1-(benzenesulfonyl)-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-pyrrolo-[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (0.26 g, 486.97 μmol, 1 eq) and benzyl 5-amino-2-methyl-piperidine-1-carboxylate (241.85 mg, 973.95 μmol, 2 eq) in NMP (0.4 mL) was added DIEA (314.69 mg, 2.43 mmol, 424.11 μL, 5 eq). The mixture was stirred at 70° C. for 2 h. The solution was cooled to 15° C., diluted with water (50 mL) and extracted with EtOAc (20 mL×3). The combined organic phase was washed with brine (30 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=5/1,2/1) to give a racemate product (0.25 g) as a yellow solid. The product was separated by SFC (column: Chiralpak AS-H 250*30 mm i.d. 5u Mobile phase: A for CO2 and B for MeOH (0.1% NH₃H₂O) Gradient: B %=40% Flow rate: 70 g/min Wavelength: 220 nm. Column temperature: 40° C. System back pressure: 100 bar Cycle time: 5 min) to afford the title compound 1 (Peak 1, RT=1.74 min, 120 mg, 160.91 μmol, 33.04% yield) as a yellow solid. Compound 2 (Peak 2, 100 mg, 134.09 μmol, 27.54% yield. It was used for example 4) as a yellow solid.

Step 4: Benzyl (2S,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.1 g, 134.09 μmol, 1 eq) in MeOH (3 mL) was added NaOH (2 M, 670.45 μL, 10 eq). The mixture was stirred at 40° C. for 1 h. The solution was cooled to 15° C. and poured into water (10 mL). The aqueous phase was extracted with EtOAc (10 mL×2). The combined organic phase was washed with brine (10 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (70 mg, crude) as a yellow solid and used directly.

Step 5: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]-amino]-2-methyl-piperidine-1-carboxylate (70 mg, 115.59 μmol, 1 eq) in DCM (5 mL) was added BBr₃ (115.83 mg, 462.34 μmol, 44.55 μL, 4 eq) at 0° C. The mixture was stirred at 15° C. for 2 h. The reaction mixture was concentrated in vacuum. The residue was washed with PE (10 mL), filtered and the filter cake was collected. The residue was purified by prep-HPLC (HCl condition) to afford the title compound (26.8 mg, 100% purity, HCl salt) as a yellow solid.

4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo-[2,3-b]-pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine is produced following steps 4 and 5, but starting with benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate.

Example 26. Synthesis of Tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate Useful in the Synthesis of Compound 126)

A mixture of tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-bromo-indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (300 mg, 440.83 μmol, 1 eq), tributyl-(3-methyltriazol-4-yl)stannane (1.31 g, 1.76 mmol, 4 eq) and Pd(dppf)Cl₂ (32.26 mg, 44.08 μmol, 0.1 eq) in dioxane (0.5 mL) was stirred for 20 h at 100° C. under N₂. The mixture was cooled to 15° C. and poured into water (10 mL) and extracted with EtOAc (20 mL×3). The combined organic layer was washed with brine (20 mL×3), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by MPLC (SiO₂, PE:EtOAc=4/1 to 1/1) to afford the title compound (280 mg, 83.6% purity) as a yellow solid. The reaction was combined with another reaction in 20 mg scale for work up.

Example 27. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-indol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 129) Step 1: 3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carbonitrile

To a solution of 2, 4-dichloro-5-(trifluoromethyl)pyrimidine (30.53 g, 140.69 mmol, 2 eq) in DCE (250 mL) was added AlCl₃ (19.70 g, 147.72 mmol, 8.07 mL, 2.1 eq). The mixture was stirred at 90° C. for 0.5 h. Then 1H-indole-6-carbonitrile (10 g, 70.34 mmol, 1 eq) was added and the resulting solution was stirred at 90° C. for 2 h. The residue was dissolved in MeOH (100 mL) and poured into ice-water (1000 mL) and stirred for 5 min. The solids were formed and filtered to collect the cake. The cake was washed with MeOH (500 mL), filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (PE:EtOAc=1:1) to afford the title compound (10 g, 26.34 mmol, 37.45% yield, 85% purity) as yellow solid.

Step 2: 3-[2-chloro-5-(trifluoromethyl) pyrimidin-4-yl]-1-(2-trimethylsilylethoxymethyl)indole-6-carbonitrile

To a solution of 3-[2-chloro-5-(trifluoromethyl) pyrimidin-4-yl]-1H-indole-6-carbonitrile (1 g, 3.10 mmol, 1 eq) in THF (20 mL) was added NaH (185.93 mg, 4.65 mmol, 60% purity, 1.5 eq) at 0° C. The mixture was stirred at 0° C. for 0.5 h. Then SEMCl (775.03 mg, 4.65 mmol, 822.75 μL, 1.5 eq) was added and the mixture was stirred at 0° C. for 1 h. The residue was poured into ice-water (50 mL). The aqueous phase was extracted with EtOAc (50 mL×3). The combined organic phase was washed with brine (50 mL×2), dried with anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography PE:EtOAc=20:1-10:1-8:1 to afford the title compound (0.7 g, 1.53 mmol, 49.37% yield, 99% purity) as white solid.

Step 3: Tert-butyl (3S)-3-[[4-[6-cyano-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of 3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1-(2-trimethylsilylethoxymethyl)indole-6-carbonitrile (0.5 g, 1.10 mmol, 1 eq), tert-butyl (3S)-3-aminopiperidine-1-carboxylate (287.42 mg, 1.44 mmol, 1.3 eq) and DIEA (428.01 mg, 3.31 mmol, 576.83 μL, 3 eq) in NMP (5 mL) was stirred at 140° C. for 1 h. The reaction mixture was diluted with H₂O (80 mL) and extracted with EtOAc (30 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated. The residue was purified by column chromatography (SiO₂, PE:EtOAc=10:1 to 2:1) to afford the title compound (0.63 g, 817.19 umol, 74.03% yield, 80% purity) as a yellow oil.

Step 4: Tert-butyl (3S)-3-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-[6-cyano-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.5 g, 810.70 μmol, 1 eq) in EtOH (5 mL) was added hydroxylamine hydrochloride (563.36 mg, 8.11 mmol, 10 eq), Na₂CO₃ (687.41 mg, 6.49 mmol, 8 eq) and the mixture was stirred at 30° C. for 12 h. The reaction mixture was diluted with H₂O (50 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (0.56 g, crude) as a yellow solid.

Step 5: Tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amin]piperidine-1-carboxylate (0.5 g, 769.49 μmol, 1 eq) in EtOH (6 mL) and EtOAc (2 mL) was added EtONa (104.73 mg, 1.54 mmol, 2 eq). The mixture was stirred at 90° C. for 30 min. The reaction mixture was concentrated to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=5:1 to 2:1) to afford the title compound (300 mg) as a yellow oil. (The reaction was combined with another reaction in 80 mg scale for purification.)

Step 6: 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-indol-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A mixture of tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-(2-trimethylsilylethoxymethyl)indol-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.25 g, 371.03 μmol, 1 eq) and H₂SO₄ (363.91 mg, 3.71 mmol, 197.78 μL, 10 eq) in dioxane (5 mL) was stirred at 40° C. for 1 h. The mixture was adjusted pH to 8 with saturated aqueous Na₂CO₃ and stirred at 20° C. for 20 min. Then the aqueous was extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (FA condition) to afford title compound (50.7 mg, FA) as a white solid.

Example 28. Synthesis of Benzyl (3S,5R)-3-amino-5-methoxy-piperidine-1-carboxylate Useful in the Synthesis of Compound 131 Step 1: benzyl (3S,5R)-3-(tert-butoxycarbonylamino)-5-methoxy-piperidine-1-carboxylate

A benzyl (3S,5R)-3-(tert-butoxycarbonylamino)-5-hydroxy-piperidine-1-carboxylate (500 mg, 1.43 mmol, 1 eq) in THF (5 mL) was added NaH (74.19 mg, 1.85 mmol, 60% purity, 1.3 eq) at 0° C. The mixture was stirred at 0° C. for 0.5 h. Then MeI (222.79 mg, 1.57 mmol, 97.71 μL, 1.1 eq) was added. The mixture was stirred for another 1 h at 15° C. It was poured into water (15 mL) and extracted with EtOAc (25 mL×3). The combined organic layer was washed with brine (25 mL×3), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by MPLC (SiO₂, PE:EtOAc=4/1 to 1/1) to afford the title compound (450 mg, 987.83 μmol, 69.23% yield, 80% purity) as brown solid.

Step 2: benzyl (3S,5R)-3-amino-5-methoxy-piperidine-1-carboxylate

A solution of benzyl (3S,5R)-3-(tert-butoxy carbonylamino)-5-methoxy-piperidine-1-carboxylate (450 mg, 1.23 mmol, 1 eq) in HCl/EtOAc (50 mL) was stirred at 15° C. for 1 h. The reaction mixture was concentrated in vacuum, the residue was dissolved into MeOH (15 mL) and adjusted pH to 9 by Amberlyst 21 to afford the title compound (350 mg, crude) as brown solid. It will be used next step without further purification.

Example 29. Synthesis of (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (Compound 133) Step 1: (3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1-benzyl-piperidin-3-ol

A mixture of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3,5-dimethyl-isoxazole (280 mg, 484.80 umol, 1 eq), (3R,5S)-5-amino-1-benzyl-piperidin-3-ol (130.01 mg, 630.24 umol, 1.3 eq) and DIEA (313.29 mg, 2.42 mmol, 422.22 uL, 5 eq) in THF (3 mL) was stirred at 15° C. for 1 h. It was poured into water (10 mL) and extracted with EtOAc (20 mL×3). The combined organic layer was washed with brine (20 mL×3), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure. The residue was purified by MPLC (SiO₂, PE/EtOAc=3/1 to 1/1) to afford the title compound (170 mg, 94% purity) as brown solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work up)

Step 2: tert-butyl (3S,5R)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate

To a solution of (3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1-benzyl-piperidin-3-ol (150 mg, 213.15 umol, 1 eq) and Boc₂O (69.78 mg, 319.72 umol, 73.45 uL, 1.5 eq) in THF (2 mL) was added Pd/C (20 mg, 10% purity) under N₂. The suspension was degassed under vacuum and purged with H₂ several times. It was stirred under H₂ (15 psi) at 15° C. for 1 h. Then the mixture was filtered though a pad of celite. The filtrate was concentrated under reduced pressure to give a residue. It was purified by MPLC (SiO₂, PE/EtOAc=4/1 to 1/1) to afford the title compound (100 mg) as yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for work up).

Step 3: tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate

A mixture of tert-butyl (3S,5R)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate (75 mg, 105.08 umol, 1 eq) and NaOH (2 M, 262.71 uL, 5 eq) in MeOH (0.2 mL) was stirred at 50° C. for 1 h and then cooled to the room temperature. It was poured into the water (10 mL), and extracted with EtOAc (20 mL×3). The combined organic layer was washed with brine (20 mL×3), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to afford the title compound (70 mg, crude) as brown solid which was used in next step without further purification

(Note: The reaction was combined with another reaction in 10 mg scale for work up)

Step 4: (3R,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

A solution of tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate (50 mg, 87.17 umol, 1 eq) in HCl/EtOAc (5 mL) was stirred at 15° C. for 1 h. It was concentrated. The crude product was purified by prep-HPLC (HCl condition) to afford the title compound (10 mg, 95.1% purity, HCl, 100% ee) as yellow solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work up)

Example 30. Synthesis of 4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 136) Step 1: 1H-pyrrolo[2,3-b]pyridine-6-carboxylic acid

To a solution of ethyl 1H-pyrrolo[2,3-b]pyridine-6-carboxylate (4.3 g, 22.61 mmol, 1 eq) in dioxane (40 mL) was added NaOH (2 M, 50 mL, 4.42 eq). The mixture was stirred at 80° C. for 1 h. The solution was concentrated under reduced pressure to remove dioxane and water. The residue was diluted with H₂O (50 mL) and adjusted pH to 2 with HCl (1M), with a lot of solid production, filtered to afford the title compound (3.5 g, crude) as a yellow solid.

Step 2: N-[(E)-N-hydroxy-C-methyl-carbonimidoyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide

To a solution of 1H-pyrrolo[2,3-b]pyridine-6-carboxylic acid (1 g, 6.17 mmol, 1 eq) in MeCN (10 mL) was added HOBt (1.67 g, 12.33 mmol, 2 eq), EDCI (2.36 g, 12.33 mmol, 2 eq), N-hydroxyacetamidine (913.77 mg, 12.33 mmol, 2 eq), and DIPEA (3.99 g, 30.84 mmol, 5.37 mL, 5 eq). The mixture was stirred at 30° C. for 12 h. Then it was concentrated under reduced pressure to afford the title compound (1.5 g, crude) as white solid which was used directly without further purification.

Step 3: 3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-oxadiazole

A solution of N-[(E)-N-hydroxy-C-methyl-carbonimidoyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide (1.5 g, 6.87 mmol, 1 eq) in Diglyme (20 mL) was stirred at 100° C. for 12 h. The reaction mixture was poured into water (200 mL) and the solid was formed. It was filtered to afford the title compound (0.4 g, crude) as brown solid.

Step 4: 5-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-1,2,4-oxadiazole

To a solution of 3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-oxadiazole (0.4 g, 2.00 mmol, 1 eq) in DMSO (dimethylsulfoxide; 4 mL) was added NBS (391.18 mg, 2.20 mmol, 1.1 eq). The mixture was stirred at 15° C. for 2 h. It was diluted with H₂O (30 mL), with a lot of solid formed. It was filtered to afford the title compound (480 mg, crude) as brown solid.

Step 5: 5-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-1,2,4-oxadiazole

To a solution of 5-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-1,2,4-oxadiazole (675 mg, 2.42 mmol, 1 eq) in DMF (7 mL) was added NaH (125.76 mg, 3.14 mmol, 60% purity, 1.3 eq). The mixture was stirred at 0° C. for 0.5 h. Then the benzenesulfonyl chloride (640.75 mg, 3.63 mmol, 464.31 uL, 1.5 eq) was added, the resulting mixture was stirred at 15° C. for 1.5 h. Then it was quenched by addition water (40 mL), with a lot of solid formed, and then it was filtered to afford the crude product. The crude product was purified by column chromatography (SiO₂, EtOAc) to afford the title compound (480 mg, 801.43 umol, 33% yield, 70% purity) as an orange solid.

Step 6: 5-[1-(benzenesulfonyl)-3-(4, 4,5, 5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-1,2,4-oxadiazole

A mixture of 5-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-1,2,4-oxadiazole (410 mg, 977.93 umol, 1 eq), BPD (372.50 mg, 1.47 mmol, 1.5 eq), KOAc (191.95 mg, 1.96 mmol, 2 eq), Pd(dppf)Cl₂ (107.33 mg, 146.69 umol, 0.15 eq) in dioxane (4 mL) was degassed and purged with N₂ for 5 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The solution was diluted with H₂O (25 mL) and extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (45 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 5/1) to afford the title compound (240 mg, 411.74 umol, 42% yield, 80% purity) as a yellow solid.

Step 7: Tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3-methyl-1,2,4-oxadiazol-5-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of 5-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-1,2,4-oxadiazole (240 mg, 411.74 umol, 1 eq), tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (172.46 mg, 452.91 umol, 1.1 eq), Na₂CO₃ (87.28 mg, 823.47 umol, 2 eq), Pd(dppf)Cl₂ (45.19 mg, 61.76 umol, 0.15 eq) in dioxane (2.5 mL) and H₂O (0.5 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1.5 h under N₂ atmosphere. The solution was concentrated under reduced pressure to remove dioxane. The residue was diluted with H₂O (30 mL) and extracted with EtOAc (15 mL×2). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=3/1 to 1/1) to afford the title compound (340 mg, 70% purity) as yellow solid.

Step 8: Tert-butyl (3S)-3-[[4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3-methyl-1,2,4-oxadiazol-5-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (80 mg, 116.84 umol, 1 eq) in MeOH (2.5 mL) was added NaOH (2 M, 292.10 uL, 5 eq). The mixture was stirred at 60° C. for 1 h. The solution was concentrated under reduced pressure to remove MeOH. The residue was diluted with H₂O (15 mL) and adjusted pH to 7 by added HCl (1M), then extracted with EtOAc (15 mL×2). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the crude product (80 mg, crude) as yellow solid.

Step 9: 4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(3-methyl-1,2,4-oxadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (60 mg, 110.19 umol, 1 eq) in EtOAc (0.5 mL) was added HCl/EtOAc (4 M, 1 mL, 36.30 eq). The mixture was stirred at 14° C. for 1 h. The solution was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (FA condition) to afford the title compound (27.3 mg, FA, 99% purity) as white solid.

Example 31. Synthesis of N-[(3S)-5, 5-dimethyl-3-piperidyl]-4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 137) Step 1: 2-[1-(benzenesulfonyl)pyrrolo[2,3-b]pyridin-6-yl]thiazole

A mixture of 1-(benzenesulfonyl)-6-bromo-pyrrolo[2,3-b]pyridine (3.1 g, 9.19 mmol, 1 eq), tributyl(thiazol-2-yl)stannane (3.78 g, 10.11 mmol, 1.1 eq), CuI (175.09 mg, 919.36 umol, 0.1 eq) and Pd(PPh₃)₄ (1.06 g, 919.36 umol, 0.1 eq) in DMF (30 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 130° C. for 12 h under N₂ atmosphere. The mixture was poured into water (300 mL) and EtOAc (200 mL), and filtered to remove the CuI. The organic layers were separated, washed with brine (150 mL), dried over Na₂SO₄ and concentrated to give a residue. It was suspended in MeOH (20 mL), and stirred 10 min at room temperature and filtered. The filter cake was collected and dried to dryness to afford the title compound (2 g, 5.27 mmol, 57% yield, 90% purity) as a brown solid.

Step 2: 2-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]thiazole

To a solution of 2-[1-(benzenesulfonyl)pyrrolo[2,3-b]pyridin-6-yl]thiazole (1.8 g, 5.27 mmol, 1 eq) in THF (18 mL) was added NBS (0.94 g, 5.27 mmol, 1 eq). The mixture was stirred at 25° C. for 12 h under N₂ atmosphere. The mixture was poured into water (80 mL) and extracted with EtOAc (30 mL×2). The organic layers were separated, washed with brine (150 mL), dried over Na₂SO₄ and concentrated to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 3/1) to afford the title compound (1.5 g) as a yellow solid.

Step 3: 2-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]thiazole

A mixture of 2-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.95 g, 2.26 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (1.15 g, 4.52 mmol, 2 eq), Pd(dppf)Cl₂ (165.39 mg, 226.03 umol, 0.1 eq) and KOAc (443.65 mg, 4.52 mmol, 2 eq) in dioxane (10 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. The mixture was poured into water (50 mL) and extracted with EtOAc (20 mL×2). The organic layers were separated, washed with brine (150 mL), dried over Na₂SO₄ and concentrated to give a residue. It was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 4/1) to afford the title compound (0.63 g, 1.15 mmol, 50% yield, 85% purity) as a yellow solid.

Step 4: 2-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]thiazole

A mixture of 2-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.05 M, 26.96 mL, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (462.27 mg, 2.02 mmol, 1.5 eq), Na₂CO₃ (285.74 mg, 2.70 mmol, 2 eq) and ditert-butyl(cyclopentyl)phosphane:dichloropalladium:iron (87.85 mg, 134.80 umol, 0.1 eq) in THF (20 mL) and H₂O (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. The reaction mixture was diluted with addition H₂O (100 mL), and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 3/1) to afford the title compound (300 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 50 mg scale for work up)

Step 5: 2-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]thiazole

A mixture of 2-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.28 g, 524.77 umol, 1 eq) and m-CPBA (266.35 mg, 1.31 mmol, 85% purity, 2.5 eq) in DCM (3 mL) was stirred at 15° C. for 3 h. The solution was washed with sat.Na₂SO₃ (30 mL), Sat.NaHCO₃ (30 mL) and brine (50 mL). The organic layers were dried over Na₂SO₄ and concentrated. The residue was washed with PE/EtOAc=3/1 (4 mL), and filtered to afford the title compound (180 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work up).

Step 6: Tert-butyl (5S)-5-[[4-[1-(benzenesulfonyl)-6-thiazol-2-yl-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,3-dimethyl-piperidine-1-carboxylate

A mixture of 2-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.16 g, 282.90 umol, 1 eq), tert-butyl (5S)-5-amino-3,3-dimethyl-piperidine-1-carboxylate (96.89 mg, 424.35 umol, 1.5 eq) and DIEA (109.69 mg, 848.71 umol, 147.83 uL, 3 eq) in THF (2 mL) was stirred at 15° C. for 1 h. The reaction mixture was concentrated to afford the title compound (300 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 10 mg scale for work up)

Step 7: Tert-butyl (5S)-3,3-dimethyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of tert-butyl (5S)-5-[[4-[1-(benzenesulfonyl)-6-thiazol-2-yl-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,3-dimethyl-piperidine-1-carboxylate (0.25 g, 350.24 umol, 1 eq) and NaOH (2 M, 1.75 mL, 10 eq) in MeOH (3 mL) was stirred at 50° C. for 0.5 h. It was diluted with H₂O (30 mL) and extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 3/1) to afford the title compound (160 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 50 mg scale for work up.)

Step 8: N-[(3S)-5,5-dimethyl-3-piperidyl]-4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

A mixture of tert-butyl (5S)-3,3-dimethyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (150 mg, 261.49 umol, 1 eq) and HCl/EtOAc (4 M, 2 mL) was stirred at 15° C. for 0.5 h. The reaction mixture was concentrated to give a residue. The residue was purified by prep-HPLC (HCl condition) to afford the title compound (21.7 mg, HCl) as a yellow solid.

(Note: The reaction was combined with another reaction in 10 mg scale for purification.)

Example 32. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 139) Step 1: N′-hydroxy-1H-pyrrolo[2,3-b]pyridine-6-carboxamidine

To a solution of 1H-pyrrolo[2,3-b]pyridine-6-carbonitrile (1 g, 6.99 mmol, 1 eq) in EtOH (30 mL) was added NH₂OH.HCl (4.85 g, 69.86 mmol, 10 eq) and Na₂CO₃ (8.89 g, 83.83 mmol, 12 eq). The mixture was stirred at 30° C. for 12 h. The suspension was filtered and concentrated under reduced pressure to afford the title compound (1.3 g, crude) as yellow solid, which was used into the next step without further purification.

Step 2: 5-methyl-3-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-oxadiazole

To a solution of N′-hydroxy-1H-pyrrolo[2,3-b]pyridine-6-carboxamidine (1.2 g, 6.81 mmol, 1 eq) in AcOH (12 mL) was added Ac₂O (1.39 g, 13.62 mmol, 1.28 mL, 2 eq). The mixture was stirred at 90° C. for 1 h. The solution was poured into H₂O (100 mL) and the yellow solid was formed. It was filtered and dried to afford the title compound (0.85 g, crude) as yellow solid, which was used into the next step without further purification.

Step 3: 3-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-5-methyl-1,2,4-oxadiazole

To a solution of 5-methyl-3-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-oxadiazole (0.8 g, 4.00 mmol, 1 eq) in THF (80 mL) was added NBS (711.24 mg, 4.00 mmol, 1 eq). The mixture was stirred at 15° C. for 2 h. The solution was poured into H₂O (100 mL), while the yellow solid was formed. It was filtered to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=1/1 to 0/1) to afford the title compound (0.4 g, 1.15 mmol, 28% yield, 80% purity) as yellow solid. (Note: The reaction was combined with another reaction in 150 mg scale for work up)

Step 4: 3-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-5-methyl-1,2,4-oxadiazole

To a solution of 3-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-5-methyl-1,2,4-oxadiazole (0.3 g, 1.07 mmol, 1 eq) in DMF (3 mL) was added NaH (64.49 mg, 1.61 mmol, 60% purity, 1.5 eq) at 0° C. The reaction mixture was stirred at 0° C. for 0.5 h. Then the benzenesulfonyl chloride (227.82 mg, 1.29 mmol, 165.09 uL, 1.2 eq) was added to the above mixture, and stirred at 15° C. for another 1.5 h. After the material was converted completely, the solution was poured into H₂O (20 mL), while the yellow solid formed. It was filtered to give the crude product. It was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (0.2 g, 429.34 umol, 39% yield, 90% purity) as yellow solid.

Step 5: 3-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1, 3 2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-5-methyl-1,2,4-oxadiazole

A mixture of 3-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-5-methyl-1,2,4-oxadiazole (0.2 g, 477.04 umol, 1 eq), BPD (181.71 mg, 715.56 umol, 1.5 eq), Pd(dppf)Cl₂ (34.91 mg, 47.70 umol, 0.1 eq), KOAc (93.64 mg, 954.08 umol, 2 eq) in dioxane (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The solution was poured into H₂O (20 mL) and extracted with EtOAc (20 mL×2). The combined organic layers were washed with brine (40 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (140 mg) as brown solid.

Step 6: Tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1,2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]aminopiperidine-1-carboxylate

A mixture of 3-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-5-methyl-1,2,4-oxadiazole (0.12 g, 257.34 umol, 1 eq), tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (97.99 mg, 257.34 umol, 1 eq), Pd(dppf)Cl₂ (18.83 mg, 25.73 umol, 0.1 eq), Na₂CO₃ (54.55 mg, 514.67 umol, 2 eq) in dioxane (1.5 mL) and H₂O (0.3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. The solution was poured into H₂O (20 mL), and extracted with EtOAc (20 mL×3). The combined organic layers were washed by brine (60 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give the residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=3/1 to 1/1) to afford the title compound (60 mg) as yellow solid.

(Note: The reaction mixture was combined with another reaction in 20 mg scale for work-up and purification).

Step 7: Tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1,2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.04 g, 58.42 umol, 1 eq) in MeOH (0.5 mL) was added NaOH (2 M, 0.5 mL, 17.12 eq). The mixture was stirred at 60° C. for 1 h. The solution was concentrated under reduced pressure to afford the title compound (40 mg, crude) as yellow solid, which was used into the next step without further purification.

(Note: The reaction was combined with another reaction in 20 mg scale for work up)

Step 8: 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A solution of tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (30 mg, 55.09 umol, 1 eq) in HCl/EtOAc (4 M, 1.50 mL, 108.91 eq) was stirred at 15° C. for 1 h. The solution was concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC to afford the title compound (8.2 mg, FA salt, 98.14% purity) as a white solid

(Note: The reaction was combined with another reaction in 10 mg scale for work up)

Example 33. Synthesis of 4-[6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 140) Step 1: 6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridine

A mixture of 1H-pyrrolo[2,3-b]pyridin-6-amine (2 g, 15.02 mmol, 1 eq), 1,1-dimethoxy-N,N-dimethyl-ethanamine (18.22 g, 136.80 mmol, 20.00 mL, 9.11 eq) was stirred at 130° C. for 1 h. The mixture was cooled to 0° C., conc. HCl (4 mL) was added dropwise, followed by acetohydrazide (6.68 g, 90.12 mmol, 6 eq) and the resulting mixture was stirred at 0° C. for 30 min. Then, the temperature was raised to 130° C. and the solution was stirred for another 2 h. The resulting solution was concentrated. The residue was purified by column chromatography (SiO₂, DCM/MeOH=70/1 to 7/1) to afford the title compound (10.5 g, crude, HCl) as a yellow oil.

(Note: The reaction was combined with another reaction in 200 mg scale for work up)

Step 2: 3-bromo-6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridine

To a solution of 6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[23-b]pyridine (10 g, 46.90 mmol, 1 eq) in DCM (200 mL) was added NBS (4.17 g, 23.45 mmol, 0.5 eq) at 0° C. The mixture was stirred at 15° C. for 1 h. The reaction mixture was diluted with H₂O (800 mL) and extracted with EtOAc (300 mL×2). The combined organic layers were washed with brine (1000 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, DCM/MeOH=50/1 to 10/1) to afford the title compound (5.5 g, 13.74 mmol, 73% purity) as a yellow solid.

(Note: The reaction was combined with another reaction in 500 mg scale for work up).

Step 3: 1-(benzenesulfonyl)-3-bromo-6-(3,5-dimethyl-1,2,4-triazol-4-yl)pyrrolo[2,3-b]pyridine

To a solution of 3-bromo-6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridine (5 g, 17.12 mmol, 1 eq) in DMF (90 mL) and THF (10 mL) was added NaH (821.54 mg, 20.54 mmol, 60% purity, 1.2 eq) at 0° C. batch wise. After addition, the mixture was stirred at this temperature for 0.5 h, and then benzenesulfonyl chloride (3.93 g, 22.25 mmol, 2.85 mL, 1.3 eq) was added dropwise at 0° C. The resulting mixture was stirred at 0° C. for 1 h. The resulting mixture was diluted with H₂O (500 mL) and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, DCM/MeOH=10/1) to afford the title compound (3.6 g) as a black brown solid.

(Note: The reaction was combined with another reaction in 500 mg scale for work up)

Step 4: [1-(benzenesulfonyl)-6-(3, 5-dimethyl-1,2, 4-triazol-4-yl) pyrrolo[2,3-b]pyridin-3-yl]boronic acid

A mixture of 1-(benzenesulfonyl)-3-bromo-6-(3,5-dimethyl-1,2,4-triazol-4-yl) pyrrolo[2,3-b]pyridine (0.8 g, 1.85 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (939.87 mg, 3.70 mmol, 2 eq), Pd(dppf)Cl₂ (135.41 mg, 185.06 umol, 0.1 eq) and KOAc (363.23 mg, 3.70 mmol, 2 eq) in dioxane (3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 2 h under N₂ atmosphere. The solution was diluted with H₂O 100 (mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue to afford the title compound (3.2 g, crude) as a brown oil.

Step 5: Tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethyl-1,2,4-triazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of [1-(benzenesulfonyl)-6-(3,5-dimethyl-1,2,4-triazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]boronic acid (2.7 g, 6.80 mmol, 1 eq), tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (864.00 mg, 2.27 mmol, 3.34 e-1 eq), Na₂CO₃ (1.44 g, 13.59 mmol, 2 eq) and Pd(dppf)Cl₂ (497.37 mg, 679.73 umol, 0.1 eq) in dioxane (5 mL) and H₂O (1 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. It was diluted with H₂O (100 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, DCM/MeOH=50/1 to 7/1) to afford the title compound (800 mg, crude) as a black brown oil.

(Note: The reaction was combined with another reaction in 500 mg scale for work up)

Step 6: Tert-butyl (3S)-3-[[4-[6-(3,5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of tert-butyl (3S)-3-[[4-[1-(benzenesulfonyl)-6-(3,5-dimethyl-1,2,4-triazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.7 g, 1.00 mmol, 1 eq) and NaOH (2 M, 5.02 mL, 10 eq) in MeOH (10 mL) was stirred at 50° C. for 0.5 h. The reaction mixture was diluted with H₂O 30 mL and extracted with EtOAc (15 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue that was purified by column chromatography (SiO₂, DCM: MeOH=50/1 to 10/1) to afford the title compound (180 mg) as a black brown oil.

(Note: The reaction was combined with another reaction in 100 mg scale for purification).

Step 7: 4-[6-(3, 5-dimethyl-1,2, 4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A mixture of tert-butyl (3S)-3-[[4-[6-(3, 5-dimethyl-1,2,4-triazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.16 g, 286.96 umol, 1 eq) and HCl/EtOAc (4 M, 3 mL, 41.82 eq) was stirred at 15° C. for 0.5 h. The mixture was concentrated to give a residue. The residue was purified by prep-HPLC (neutral condition) to afford the title compound (19.9 mg, free) as a white solid. (Note: The reaction was combined with another reaction in 20 mg scale for purification.)

Example 34. Synthesis of 4-[6-(5-methyltetrazol-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 141) Step 1: 2-[(6-bromopyrrolo[2,3-b]pyridin-1-yl)methoxy]ethyl-trimethyl-silane

To a solution of 6-bromo-1H-pyrrolo[2,3-b]pyridine (1.5 g, 7.61 mmol, 1 eq) in DMF (13.5 mL) and THF (1.5 mL) was added NaH (365.42 mg, 9.14 mmol, 60% purity, 1.2 eq) at 0° C., the mixture was stirred at 0° C. for 0.5 h. Then SEM-Cl (1.65 g, 9.90 mmol, 1.75 mL, 1.3 eq) was added, the mixture was stirred at 15° C. for 11.5 h. The reaction mixture was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜8% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (2.1 g, 6.42 mmol, 84.28% yield) as yellow oil.

Step 2: trimethyl-[2-[[6-(5-methyltetrazol-1-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of 2-[(6-bromopyrrolo[2,3-b]pyridin-1-yl)methoxy]ethyl-trimethyl-silane (2.1 g, 6.42 mmol, 1 eq), 5-methyl-1H-tetrazole (539.48 mg, 6.42 mmol, 1 eq), CuI (488.79 mg, 2.57 mmol, 0.4 eq), K₂CO₃ (2.13 g, 15.40 mmol, 2.4 eq) and (1S,2S)—N1,N2-dimethylcyclohexane-1,2-diamine (365.06 mg, 2.57 mmol, 0.4 eq) in DMF (20 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 130° C. for 12 h under N₂ atmosphere. It was cooled to the room temperature. The mixture was diluted with H₂O (70 mL) and extracted with EtOAc (50 mL×3). The combined organic layers were washed with brine (80 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash® Silica Flash Column, Eluent of 0˜35% Ethyl acetate/Petroleum ether gradient @ 100 mL/min) to afford the title compound (1.2 g, 3.63 mmol, 56.60% yield) as a yellow solid.

Step 3: 2-[[3-bromo-6-(5-methyltetrazol-1-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a solution of trimethyl-[2-[[6-(5-methyltetrazol-1-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (1.2 g, 3.63 mmol, 1 eq) in DMF (4.5 mL) was added NBS (710.95 mg, 3.99 mmol, 1.1 eq). The mixture was stirred at 15° C. for 2 h. The solution was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜8% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (1 g, 2.44 mmol, 67% yield) as a yellow solid.

Step 4: Trimethyl-[2-[[6-(5-methyltetrazol-1-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of 2-[[3-bromo-6-(5-methyltetrazol-1-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane (850 mg, 2.08 mmol, 1 eq), BPD (790.93 mg, 3.11 mmol, 1.5 eq), Pd(dppf)Cl₂ (151.93 mg, 207.64 umol, 0.1 eq), KOAc (407.56 mg, 4.15 mmol, 2 eq) in dioxane (10 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. It was cooled to the room temperature. The reaction mixture was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜8% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (600 mg, 47% purity) as colorless oil.

(Note: The reaction was combined with another reaction in 90 mg scale for work up)

Step 5: Tert-butyl (3S)-3-[[4-[6-(5-methyltetrazol-1-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of trimethyl-[2-[[6-(5-methyltetrazol-1-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (600 mg, 1.31 mmol, 1 eq), tert-butyl(3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (300.35 mg, 788.75 umol, 0.6 eq), Pd(dppf)Cl₂ (96.19 mg, 131.46 umol, 0.1 eq), Na₂CO₃ (278.66 mg, 2.63 mmol, 2 eq) in dioxane (6 mL) and H₂O (1.2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 12 h under N₂ atmosphere. It was cooled to the room temperature. The reaction mixture was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column, Eluent of 0˜30% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (200 mg, 296.39 umol, 22% yield) as a yellow oil.

Step 6: 4-[6-(5-methyltetrazol-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(5-methyltetrazol-1-yl)-1-(2-trimethylsilylethoxy methyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (200 mg, 296.39 umol, 1 eq) in dioxane (2 mL) was added H₂SO₄ (296.63 mg, 2.96 mmol, 161.21 uL, 98% purity, 10 eq). The mixture was stirred at 40° C. for 2 h. It was diluted with H₂O (10 mL) and adjusted to pH=12 with aq. NaOH (4 N), then extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (10 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by twice prep-HPLC (FA condition and neutral condition) to afford the title compound (4.3 mg, free) as a white solid. (Note: The reaction was combined with another reaction in 20 mg scale for purification and work up.)

Example 35. Synthesis of 4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl-5-(trifluoromethyl)pyrimidin-2-amine (Compound 142) Step 1: 1H-pyrrolo[2,3-b]pyridine-6-carbothioamide

To a solution of 1H-pyrrolo[2,3-b]pyridine-6-carbonitrile (2 g, 13.97 mmol, 1 eq) in MeOH (20 mL) and THF (10 mL) was added ammonium sulfide (1.71 g, 25.15 mmol, 1.72 mL, 1.8 eq) at 15° C. Then the solution was stirred at 15° C. for 12 h under N₂ atmosphere. The solution was quenched by addition of H₂O (30 mL) at 15° C., and extracted with EtOAc (30 mL×2). The combined organic layers were washed with brine (20 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=30/1 to 1/1) to afford the title compound (1 g, 5.64 mmol, 40.38% yield) as a yellow solid. (Note: The reaction was combined with another reaction (ET19050-19) in 1 g scale for purification and work up.)

Step 2: (NE)-N-[1-(dimethylamino)ethylidene]-1H-pyrrolo[2,3-b]pyridine-6-carbothioamide

To a solution of 1H-pyrrolo[2,3-b]pyridine-6-carbothioamide (1 g, 5.64 mmol, 1 eq) in DCM (10 mL) was added 1, 1-dimethoxy-N, N-dimethyl-ethanamine (751.52 mg, 5.64 mmol, 824.94 uL, 1 eq) at 15° C. The solution was stirred at 15° C. for 12 h. It was concentrated under reduced pressure to afford the title compound (1.3 g, crude) as a yellow solid which was used into next step without further purification. (Note: The reaction was combined with another reaction in 1.2 g scale for work up.)

Step 3: 3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-thiadiazole

To a solution of (NE)-N-[1-(dimethylamino)ethylidene]-1H-pyrrolo[2,3-b]pyridine-6-carbo thioamide (1.3 g, 5.28 mmol, 1 eq) in EtOH (10 mL) was added a solution of Py (1 mL) and amino hydrogen sulfate (2.03 g, 17.96 mmol, 3.40 eq) in MeOH (10 mL). The mixture was stirred at 15° C. for 3 h under N₂ atmosphere. The reaction mixture was quenched by addition H₂O (20 mL) at 15° C., and extracted with EtOAc (30 mL×2). The combined organic layers were washed with brine (20 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=30/1 to 1/1) to afford the title compound (1 g, 4.62 mmol, 87.62% yield) as a yellow solid. (Note: The reaction was combined with another reaction in 450 mg scale for purification and work up.)

Step 4: 5-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-1,2,4-thiadiazole

To a solution of 3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-6-yl)-1,2,4-thiadiazole (1 g, 4.62 mmol, 1 eq) in DCM (10 mL) was added Br₂ (738.96 mg, 4.62 mmol, 238.37 uL, 1 eq) at 0° C. The mixture was degassed and purged with N₂ for 3 times and stirred at 0° C. for 1 h under N₂ atmosphere. The reaction was concentrated under reduced pressure to give a residue. It was triturated with MTBE (methyl tert-butyl ether) at 15° C. for 10 min to afford title compound (1.2 g, 2.03 mmol, 43.96% yield, 50% purity) as a yellow solid. (Note: The reaction was combined with another reaction in 290 mg scale for purification and work up.)

Step 5: 2-[[3-bromo-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a solution of 5-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-1,2,4-thiadiazole (1.2 g, 4.07 mmol, 1 eq) in THF (10 mL) was added NaH (325.22 mg, 8.13 mmol, 60% purity, 2 eq) and 2-(chloromethoxy)ethyl-trimethyl-silane (1.36 g, 8.13 mmol, 1.44 mL, 2 eq) at 0° C. Then the mixture was stirred at 0° C. for 1 h under N₂ atmosphere. The reaction mixture was quenched by addition of H₂O (20 mL) at 15° C., and extracted with EtOAc (20 mL×2). The combined organic layers were washed with (20 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=30/1 to 1/1) to afford the title compound (1.1 g, 2.33 mmol, 57.24% yield, 90% purity) as a yellow solid.

Step 6: Trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of 2-[[3-bromo-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]m ethoxy]ethyl-trimethyl-silane (500 mg×2, 1.18 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (447.69 mg, 1.76 mmol, 1.5 eq), Pd(dppf)Cl₂ (86.00 mg, 117.53 umol, 0.1 eq), KOAc (230.70 mg, 2.35 mmol, 2 eq) in dioxane (8 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The reaction mixture was quenched by addition of H₂O (10 mL) at 15° C., and extracted with EtOAc (20 mL×2). The combined organic layers were washed with brine (10 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=30/1 to 1/1) to afford the title compound (800 mg, 541.82 umol, 23.05% yield, 32% purity) as a black brown solid

Step 7: Tert-butyl(3S)-3-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (800 mg, 1.69 mmol, 1 eq), tert-butyl(3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (644.75 mg, 1.69 mmol, 1 eq), Na₂CO₃ (358.92 mg, 3.39 mmol, 2 eq), Pd(dppf)Cl₂ (123.89 mg, 169.32 umol, 0.1 eq) in dioxane (10 mL) and H₂O (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 3 h under N₂ atmosphere. The resulting mixture was quenched by addition H₂O (10 mL) at 15° C. and extracted with EtOAc (20 mL×2). The combined organic layers were washed with brine (15 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=30/1 to 5/1) to afford the title compound (150 mg, 136.79 umol, 8.08% yield, 63% purity) as a brown solid.

Step 8: 4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifleoromethyl)pyrimidin-2-yl]amino]piperidin e-1-carboxylate (150 mg, 217.12 umol, 1 eq) in dioxane (1 mL) was added H₂SO₄ (217.30 mg, 2.17 mmol, 118.10 uL, 98% purity, 10 eq). The mixture was degassed and purged with N₂ for 3 times and stirred at 40° C. for 3 h under N₂ atmosphere. The reaction mixture was quenched by addition of H₂O (10 mL) at 15° C., and extracted with EtOAc (15 mL×2). The organic layer was concentrated to give crude residue, which was dissolved in H₂O (5 mL). NaOH was added to adjust pH to 12. The mixture was stirred for 10 min at 15° C. The stirred solution was extracted with EtOAc (10 mL×2). The combined organic layers were washed with brine (10 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (HCl condition) to afford the title compound (6.7 mg, HCl salt 95% purity) as a yellow solid.

Example 36. Synthesis of (3R, 5S)—N-methyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxamide (Compound 145) Step 1: O1-tert-butyl O3-methyl-(3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-thiazol-2-yl-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1,3-dicarboxylate

A mixture of 2-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]thiazole (0.28 g, 495.08 umol, 1 eq), O1-tert-butyl O3-methyl (3R)-5-aminopiperidine-1,3-dicarboxylate (191.83 mg, 742.62 umol, 1.5 eq) and DIEA (191.95 mg, 1.49 mmol, 258.70 uL, 3 eq) in THF (5 mL) was stirred at 15° C. for 30 min. The reaction mixture was diluted with H₂O (50 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 1/1) to afford the title compound (260 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work up)

Step 2: (3R, 5S)-1-tert-butoxycarbonyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxylic acid

To a solution of O1-tert-butyl O3-methyl (3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-thiazol-2-yl-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1,3-dicarboxylate (240 mg, 322.68 umol, 1 eq) in MeOH (5 mL) was added NaOH (2 M, 1.61 mL, 10 eq). The mixture was stirred at 15° C. for 30 min. The reaction mixture was adjusted pH to 4 with aqueous HCl (0.5 M), and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (90 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (170 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work up).

Step 3: Tert-butyl (3R, 5S)-3-(methylcarbamoyl)-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of (3R,5S)-1-tert-butoxycarbonyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxylic acid (140 mg, 237.45 umol, 1 eq) in DMF (2 mL) was added HATU ((Dimethylamino)-N,N-dimethyl(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yloxy)methaniminium hexafluorophosphate; 135.43 mg, 356.18 umol, 1.5 eq), DIEA (92.07 mg, 712.36 umol, 124.08 uL, 3 eq), methanamine (2 M, 356.18 uL, 3 eq). The mixture was stirred at 15° C. for 1 h. The reaction mixture was poured into saturated aqueous NaHCO₃ (20 mL), stirred for 5 min. Then, the solid was formed. It was filtered to afford the title compound (160 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 10 mg scale for work up)

Step 4: (3R, 5S)—N-methyl-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-3-carboxamide

A mixture of tert-butyl (3R,5S)-3-(methylcarbamoyl)-5-[[4-(6-thiazol-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (150 mg, 248.91 umol, 1 eq) and HCl/EtOAc (4 M, 3 mL) was stirred at 15° C. for 30 min. The mixture was concentrated to give a residue. It was purified by prep-HPLC (neutral condition) to afford the title compound (19.4 mg) as a white solid. (Note: The reaction was combined with another reaction in 10 mg scale for purification).

Example 37. Synthesis of (3R, 5S)-5-[[4-[6-(3, 5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (Compound 146) Step 1: (3R, 5S)-1-benzyl-5-[[4-[6-(3, 5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

A mixture of 3,5-dimethyl-4-[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-6-yl]isoxazole (0.25 g, 478.47 umol, 1 eq), (3R,5S)-5-amino-1-benzyl-piperidin-3-ol (98.70 mg, 478.47 umol, 1 eq), DIEA (185.51 mg, 1.44 mmol, 250.02 uL, 3 eq) in THF (5 mL) was stirred at 15° C. for 1 h. The mixture was poured into water (20 mL), and then extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 0/1) to afford the title compound (190 mg) as a yellow solid

Step 2: Tert-butyl (3S, 5R)-3-[[4-[6-(3, 5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate

To a solution of (3R,5S)-1-benzyl-5-[[4-[6-(3, 5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (0.17 g, 262.07 umol, 1 eq) tert-butoxycarbonyl tert-butyl carbonate (171.59 mg, 786.22 umol, 180.62 uL, 3 eq) in MeOH (1 mL) was added Pd/C (10%, 0.2 g) under N₂. The suspension was degassed under vacuum and purged with H₂ several times. It was stirred at 15° C. for 16 h under H₂ atmosphere (15 psi). The reaction mixture was filtered and the filter was concentrated. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 0/1) to afford the title compound (90 mg) as a white solid. (Note: The reaction was combined with another reaction in 20 mg scale for work up.)

Step 3: (3R, 5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

A mixture of tert-butyl (3S,5R)-3-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate (80 mg, 121.46 umol, 1 eq) in HCl/MeOH (4 M, 910.93 uL, 30 eq) was stirred at 60° C. for 16 h. It was concentrated and the residue was purified by prep-HPLC to afford the title compound (20 mg, 99.47% purity, FA) as a white solid. (Note: The reaction was combined with another reaction in 10 mg scale for work up.)

Example 38. Synthesis of (3R,5S)-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol (Compound 148) Step 1: 3-methyl-4-(1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

A mixture of 6-bromo-1H-pyrrolo[2,3-b]pyridine (1 g, 5.08 mmol, 1 eq), 3-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)isoxazole (1.11 g, 5.33 mmol, 1.05 eq), Pd(dppf)Cl₂—CH₂Cl₂ (207.24 mg, 253.77 umol, 0.05 eq), NaHCO₃ (1.28 g, 15.23 mmol, 592.19 uL, 3 eq) in DME (10 mL) and H₂O (4 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 12 h under N₂ atmosphere. It was cooled to the room temperature. The reaction mixture was diluted with H₂O (30 mL) and extracted with DCM (20 mL×3). The combined organic layers were washed with brine (20 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column, Eluent of 0˜15% Ethyl acetate/Petroleum ether gradient @ 50 mL/min) to afford the title compound (800 mg) as a yellow solid. (Note: The reaction was combined with another reaction (ET12872-179) in 50 mg scale for purification and work up.)

Step 2: 4-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-isoxazole

To a solution of 3-methyl-4-(1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (720 mg, 3.61 mmol, 1 eq) in DMF (7 mL) was added NBS (771.93 mg, 4.34 mmol, 1.2 eq). The mixture was stirred at 15° C. for 2 h. The reaction mixture was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine 50 (mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash® Silica Flash Column, Eluent of 0˜25% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (600 mg, 2.16 mmol, 59.69% yield) as a colorless oil.

Step 3: 4-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

To a solution of 4-(3-bromo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methyl-isoxazole (600 mg, 2.16 mmol, 1 eq) in DMF (5 mL) and THF (0.5 mL) was added NaH (129.44 mg, 3.24 mmol, 60% purity, 1.5 eq). The mixture was stirred at 15° C. for 10 min. Then benzenesulfonyl chloride (495.37 mg, 2.80 mmol, 358.96 uL, 1.3 eq) was added, the mixture was stirred at 15° C. for 2.3 h. The reaction mixture was diluted with H₂O (60 mL) and EtOAc (30 mL). Then it was filtered. The filtrate was partitioned and the water layer was extracted with EtOAc (30 mL×2). The filter cake and the combined organic layers were concentrated under reduced pressure to give a residue. The residue was diluted with MeOH (30 mL) and stirred for 20 min. The reaction mixture was filtered and the filter cake was dried in vacuum to afford the title compound (800 mg, 1.91 mmol, 88.65% yield) was obtained as a brown solid

Step 4: 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

A mixture of 4-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (670.00 mg, 1.60 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (610.16 mg, 2.40 mmol, 1.5 eq), Pd(dppf)Cl₂ (117.21 mg, 160.19 umol, 0.1 eq), KOAc (314.41 mg, 3.20 mmol, 2 eq) in dioxane (8 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. It was cooled to the room temperature. The mixture was diluted with dioxane (30 mL) and filtered. The filtrate was concentrated under reduced pressure to afford the title compound (800 mg, crude) was obtained as a brown solid, and it was used into the next step without further purification.

Step 5: 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

A mixture of 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (800 mg, 1.03 mmol, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (235.83 mg, 1.03 mmol, 1 eq), Pd(dppf)Cl₂ (75.48 mg, 103.15 umol, 0.1 eq), Na₂CO₃ (218.66 mg, 2.06 mmol, 2 eq) in dioxane (10 mL) and H₂O (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 12 hr under N₂ atmosphere. It was cooled to the room temperature. The reaction mixture was diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (60 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜30% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (200 mg, 150.51 umol, 14.59% yield, 40% purity) was obtained as a yellow solid. (Note: The reaction was combined with another reaction in 120 mg scale for purification and work up.)

Step 6: 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (180 mg, 338.65 umol, 1 eq) in EtOAc (10 mL) was added Oxone (1.04 g, 1.69 mmol, 5 eq). The mixture was stirred at 80° C. for 12 h. It was cooled to the room temperature. The reaction mixture was filtered and the filtrate was quenched by saturation Na₂SO₃ (30 mL). The water layer was extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtrate and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜50% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (40 mg) as a white solid.

Step 7: (3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1-benzyl-piperidin-3-ol

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (35 mg, 62.11 umol, 1 eq) and DIPEA (40.14 mg, 310.54 umol, 54.09 uL, 5 eq) in THF (0.5 mL) was added (3R,5S)-5-amino-1-benzyl-piperidin-3-ol (12.81 mg, 62.11 umol, 1 eq). The mixture was stirred at 15° C. for 3 h. The reaction mixture was concentrated under reduced pressure to remove solvent. The residue was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash® Silica Flash Column, Eluent of 0-2% Dichloromethane/Methanol @ 50 mL/min) to afford the title compound (27 mg) was obtained as a white solid. (Note: The reaction was combined with another reaction in 5 mg scale for purification and work up.)

Step 8: Tert-butyl (3S,5R)-3-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridine-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate

A mixture of (3R,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1-benzyl-piperidin-3-ol (22 mg, 31.90 umol, 1 eq), Boc₂O (10.44 mg, 47.85 umol, 10.99 uL, 1.5 eq), Pd/C (50 mg, 10% purity) in THF (0.5 mL) was degassed and purged with H₂ for 3 times, and then the mixture was stirred at 15° C. for 12 h under H₂ atmosphere (15 psi). The reaction mixture was filtered and concentrated under reduced pressure to afford the title compound (30 mg, crude) as yellow oil, and it was used into the next step without further purification.

Step 9: Tert-butyl (3R,5S)-3-hydroxy-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S,5R)-3-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-5-hydroxy-piperidine-1-carboxylate (30 mg, 42.88 umol, 1 eq) in MeOH (0.5 mL) was added NaOH (2 M, 0.4 mL). The mixture was stirred at 60° C. for 0.5 h. It was cooled to the room temperature. The reaction mixture was diluted with H₂O (10 mL) and extracted with EtOAc (10 mL×4). The combined organic layers were washed with brine (20 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash® Silica Flash Column, Eluent of 0˜8% Dichloromethane/Methanol @ 50 mL/min) to afford the title compound (5 mg, 8.94 umol, 20.84% yield) as a white solid.

Step 10: (3R, 5S)-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidin-3-ol

To a solution of tert-butyl (3R,5S)-3-hydroxy-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (4 mg, 7.15 umol, 1 eq) in EtOAc (0.5 mL) was added HCl/EtOAc (4 M, 0.5 mL, 279.77 eq). The mixture was stirred at 15° C. for 0.5 h. The reaction mixture was concentrated under reduced pressure to remove solvent. The residue was purified by prep-HPLC to afford the title compound (FA, 2 mg, 94.37% purity) was obtained as a white solid. (Note: The reaction was combined with another reaction in 1 mg scale for purification and work up.)

Example 39. Synthesis of N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 150) Step 1: 1-(benzenesulfonyl)-6-bromo-pyrrolo[2,3-b]pyridine

To a solution of 6-bromo-1H-pyrrolo[2,3-b]pyridine (2 g, 10.15 mmol, 1 eq) in THF (30 mL) was added NaH (608.98 mg, 15.23 mmol, 60% purity, 1.5 eq) at −10° C. The mixture was stirred at −10° C. to 0° C. for 0.5 h. Then benzenesulfonyl chloride (2.15 g, 12.18 mmol, 1.56 mL, 1.2 eq) was added to the above and the resulting mixture was stirred at 0° C. for 1 h. It was poured into water (50 mL). The aqueous phase was extracted with EtOAc (50 mL×3). The combined organic phase was washed with brine (50 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was washed with MeOH (8 mL), filtered and the filter cake was collected to afford the title compound (3.0 g, 7.83 mmol, 77.13% yield, 88% purity) as a white solid.

Step 2: 1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine

To a solution of 1-(benzenesulfonyl)-6-bromo-pyrrolo[2,3-b]pyridine (1.1 g, 3.26 mmol, 1 eq) and tributyl-(3-methyltriazol-4-yl) stannane (3.40 g, 4.57 mmol, 1.4 eq) in DMF (30 mL) was added Pd(PPh₃)₄ (376.97 mg, 326.22 umol, 0.1 eq) and CuI (62.13 mg, 326.22 umol, 0.1 eq). The mixture was stirred at 130° C. under N₂ for 12 h. The reaction mixture was cooled to r.t., and poured into water (50 mL). The aqueous phase was extracted with EtOAc (50 mL×3). The combined organic phase was washed with brine (100 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, Petroleum ether/EtOAc=5/1, 0/1) to afford 1 g product with 77% purity. Then the product was washed with MeOH (5 mL), filtered and the filter cake was collected to afford the title compound (0.9 g, 2.39 mmol, 73.16% yield, 90% purity) as a yellow solid.

Step 3:6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridine

To a solution of 1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine (0.7 g, 2.06 mmol, 1 eq) in dioxane (15 mL) was added NaOH (2 M, 5.16 mL, 5 eq). The mixture was stirred at 90° C. for 1 h. The mixture was diluted with water (10 mL), extracted with EtOAc (15 mL×3). The combined organic phase was washed with brine (10 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (0.5 g, crude) as a yellow solid and used directly in next step.

Step 4: 3-bromo-6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridine

To a solution of 6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridine (0.5 g, 2.51 mmol, 1 eq) in DMF (10 mL) was added NBS (446.72 mg, 2.51 mmol, 1 eq). The mixture was stirred at 15° C. for 12 h. The residue was poured into water (100 mL) and stirred for 5 min. The solid was formed and filtered. The filter cake was collected to afford the title compound (0.7 g, crude) as a yellow solid which was used in next step directly.

Step 5:1-(benzenesulfonyl)-3-bromo-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine

To a solution of 3-bromo-6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridine (0.65 g, 2.34 mmol, 1 eq) in DMF (9 mL)/THF (1 mL) was added NaH (140.22 mg, 3.51 mmol, 60% purity, 1.5 eq) at 0° C. After 0.5 h, benzenesulfonyl chloride (619.20 mg, 3.51 mmol, 448.70 uL, 1.5 eq) was added and the resulting mixture was stirred at 0° C. for 1 h. It was poured into water (100 mL) and stirred for 5 min. The mixture was filtered and the filter cake was collected. It was triturated with MeOH (5 mL) and filtered to give the crude product. It was purified by silica gel chromatography (PE:EtOAc=1:1-0:1) to afford the title compound (1 g, crude) as a pink solid.

Step 6:1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridine

To a solution of 1-(benzenesulfonyl)-3-bromo-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine (0.7 g, 1.67 mmol, 1 eq), BPD (637.47 mg, 2.51 mmol, 1.5 eq) in dioxane (15 mL) was added KOAc (328.49 mg, 3.35 mmol, 2 eq) and Pd(dppf)Cl₂ (122.46 mg, 167.36 umol, 0.1 eq). The mixture was stirred at 100° C. under N₂ atmosphere for 2 h. It was cooled to r.t., and poured into water (30 mL). The aqueous phase was extracted with EtOAc (30 mL×3). The combined organic phase was washed with brine (30 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=5/1, 1/1) to afford the title compound (0.4 g, batch 1) as a white solid. Batch 2: (0.2 g) was obtained as a yellow solid which contained some de-Br product.

Step 7:1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine

To a solution of 1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridine (0.05 M, 25.79 mL, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (294.79 mg, 1.29 mmol, 1 eq) in H₂O (2 mL)/THF (16 mL) was added Na₂CO₃ (273.32 mg, 2.58 mmol, 2 eq) and ditertbutyl (cyclopentyl)phosphane;dichloropalladium;iron (84.04 mg, 128.94 umol, 0.1 eq). The mixture was stirred at 80° C. under N₂ for 1 h. It was cooled to r.t. and poured into water (50 mL). The aqueous phase was extracted with ethyl acetate (50 mL×3). The combined organic phase was washed with brine (50 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, PE/EtOAc=10/1, 0/1, contained 10% DCM) to afford the title compound (0.43 g, 647.19 umol, 50.19% yield, 80% purity) as a yellow solid.

Step 8:1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine

To a solution of 1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine (0.41 g, 771.35 umol, 1 eq) in DCM (20 mL) was added m-CPBA (391.50 mg, 1.93 mmol, 2.5 eq). The mixture was stirred at 15° C. for 12 h. The solution was quenched by sat.NaHCO₃ (20 mL) and sat.Na₂SO₃ (20 mL). The mixture was stirred for 5 min. The aqueous phase was extracted with DCM (30 mL×3). The combined organic phase dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was washed with a mixture of Petroleum ether/EtOAc=3/1 (5 mL), filtered and the filter cake was collected to afford the title compound (0.35 g, crude) as a yellow solid and used directly.

Step 9: Benzyl(2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)pyrrolo[2,3-b]pyridine-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (Product 1) and Benzyl(2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (Product 2)

To a solution of 1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridine (0.35 g, 621.08 umol, 1 eq) and benzyl 5-amino-2-methyl-piperidine-1-carboxylate (308.45 mg, 1.24 mmol, 2 eq) in THF (15 mL) was added DIEA (401.35 mg, 3.11 mmol, 540.91 uL, 5 eq). The mixture was stirred at 15° C. for 12 h. The resulting mixture was poured into water (30 mL). The aqueous phase was extracted with EtOAc (30 mL×2). The combined organic phase was washed with brine (30 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue was purified by silica gel chromatography (100-200 mesh silica gel, Petroleum ether/EtOAc=10/1, 1/1) to afford a racemate product (150 mg). Then the product was separation by SFC (column: DAICEL CHIRALPAK AS-H (250 mm*30 mm, 5 um); mobile phase:[0.1% NH₃H₂O MeOH]; B %: 45%-45%, 5 min) to afford product 1 (peak 1: RT=1.71 min, 70 mg, 80.36 umol, 12.94% yield, 84% purity) as a yellow solid, and product 2 (peak 2: 50 mg, 64.23 umol, 10.34% yield, 94% purity) as a yellow solid.

Step 10: (2S,5S)-2-methyl-5-[[4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl) pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (50 mg, 68.33 umol, 1 eq) in dioxane (4 mL) was added NaOH (2 M, 170.82 uL, 5 eq). The mixture was stirred at 90° C. for 1 h. It was cooled to 15° C. and poured into water (20 mL). The aqueous phase was extracted with EtOAc (20 mL×3). The combined organic phase was washed with brine (20 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (50 mg, crude) as a yellow solid and used directly.

(Note: The reaction was combined with another batch in 20 mg scale for purification.)

Step 11: N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (50 mg, 84.52 umol, 1 eq) in DCM (5 mL) was added BBr₃ (105.87 mg, 422.59 umol, 40.72 uL, 5 eq). The mixture was stirred at 15° C. for 2 h. The mixture was concentrated in vacuum. The residue was washed with a mixture solution of Petroleum ether/EtOAc=3/1 (15 mL), filtered and the filter cake was collected. Then the filter cake was dissolved with MeOH (1 mL) and purified by prep-HPLC (HCl) to afford the title compound (20.6 mg, 99% purity, HCl) as a yellow solid. (Note: The reaction was combined with another batch in 20 mg scale for purification.)

Example 40. Synthesis of N-[(3R,6R)-6-methyl-3-piperidyl]-4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 151) Step 1: (2R,5R)-2-methyl-5-[[4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2R, 5R)-5-[[4-[1-(benzenesulfonyl)-6-(3-methyltriazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (50 mg, 68.33 umol, 1 eq) in dioxane (4 mL) was added NaOH (2 M, 170.82 uL, 5 eq). The mixture was stirred at 90° C. for 1 h. The reaction mixture was cooled to r.t. and poured into water (20 mL).The aqueous phase was extracted with EtOAc (20 mL×3). The combined organic phase was washed with brine (20 mL×2), dried over anhydrous Na₂SO₄, filtered and concentrated in vacuum to afford the title compound (50 mg, crude) as a yellow solid and used directly.

Step 2: N-[(3R, 6R)-6-methyl-3-piperidyl]-4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R, 5R)-2-methyl-5-[[4-[6-(3-methyltriazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (50 mg, 84.52 umol, 1 eq) in DCM (5 mL) was added BBr₃ (105.87 mg, 422.59 umol, 40.72 uL, 5 eq) at 0° C. The mixture was stirred at 0° C. for 2 h. The mixture was concentrated in vacuum. The residue was washed with a mixture solution of Petroleum ether/EtOAc=3/1 (15 mL), filtered and the filter cake was collected. Then the filter cake was dissolved with MeOH (1 mL) and purified by prep-HPLC (HCl) to afford the title compound (21 mg, 42.41 umol, 50.17% yield, 99.74% purity, HCl) as a yellow solid.

Example 41. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 152) Step 1: Benzyl(2S,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 3,5-dimethyl-4-[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-6-yl]isoxazole (178.85 mg, 342.30 umol, 1 eq) in THF (1 mL) was added DIPEA (132.72 mg, 1.03 mmol, 178.86 uL, 3 eq) and benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (0.17 g, 684.60 umol, 2 eq). The mixture was stirred at 15° C. for 1 h. The reaction mixture concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/EtOAc=2/1) to afford the title compound (150 mg) as a white solid.

Step 2: Benzyl(2S,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl(2S,5S)-5-[[4-[6-(3, 5-dimethylisoxazol-4yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.15 g, 217.17 umol, 1 eq) in MeOH (2 mL) was added HCl/MeOH (4 M, 54.29 uL, 1.00 eq). The mixture was stirred at 60° C. for 12 h. The reaction mixture was concentrated under reduced pressure to afford the title compound (120 mg) as a yellow solid.

Step 3: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.1 g, 164.85 umol, 1 eq) in DCM (0.2 mL) was added BBr₃ (82.60 mg, 329.71 umol, 31.77 uL, 2 eq) at 0° C. The mixture was stirred at 0° C. for 1 h. The reaction mixture was concentrated. The residue was purified by prep-HPLC to afford the title compound (37.6 mg, HCl salt, 100% purity) as a yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for work-up and purification).

Example 42. Synthesis of 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 153) Step 1: benzyl (2R,5R)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 3,5-dimethyl-4-[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-6-yl]isoxazole (157.81 mg, 302.03 umol, 1 eq) in THF (1 mL) was added DIPEA (117.10 mg, 906.09 umol, 157.82 uL, 3 eq) and benzyl (2R,5R)-5-amino-2-methyl-piperidine-1-carboxylate (0.15 g, 604.06 umol, 2 eq).The mixture was stirred at 15° C. for 1 h. The reaction mixture concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=2/1) to afford the title compound (140 mg) as a white solid.

Step 2: benzyl (2R,5R)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl (2R,5R)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (120.00 mg, 173.73 umol, 1 eq) in MeOH (0.2 mL) was added HCl/MeOH (4 M, 1 mL). The mixture was stirred at 60° C. for 12 h. It was concentrated under reduced pressure to afford the title compound (110 mg) as a yellow solid.

Step 3: 4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R,5R)-5-[[4-[6-(3,5-dimethylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.09 g, 148.37 umol, 1 eq) in DCM (2 mL) was added BBr₃ (74.34 mg, 296.74 umol, 28.59 uL, 2 eq) at 0° C. The mixture was stirred at 0° C. for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (HCl condition) to afford the title compound (21.7 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 20 mg scale for work-up and purification).

Example 43. Synthesis of N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 154) Step 1: Trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(5-methyl-1,3,4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of trimethyl-[2-[[6-(5-methyl-1, 3,4-thiadiazol-2-yl)-3-(4,4,5, 5-tetramethyl-1,3, 2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.05 M, 22.86 mL, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (261.29 mg, 1.14 mmol, 1 eq), Na₂CO₃ (242.27 mg, 2.29 mmol, 2 eq) and ditert-butyl (cyclopentyl)phosphane:dichloropalladium:iron (74.49 mg, 114.29 umol, 0.1 eq) in THF (20 mL) and H₂O (2 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. It was diluted by addition H₂O (100 mL), and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 5/1) to afford the title compound (150 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for purification.)

Step 2: Trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(5-methyl-1,3,4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(5-methyl-1,3,4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (140 mg, 259.89 umol, 1 eq) in DCM (3 mL) was added m-CPBA (131.91 mg, 649.73 umol, 85% purity, 2.5 eq).The mixture was stirred at 15° C. for 3 h. The solution was washed with Sat.Na₂SO₃ (30 mL), Sat.NaHCO₃ (30 mL), brine (50 mL). The organic layers were dried over Na₂SO₄ and concentrated. The residue was washed with PE/EtOAc=5/1 (5 mL) and filtered to afford the title compound (120 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 10 mg scale for purification.)

Step 3: Benzyl(2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(5-methyl-1,3,4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.12 g, 210.27 umol, 1 eq) in THF (2 mL) was added DIEA (81.53 mg, 630.82 umol, 109.88 uL, 3 eq), benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (104.43 mg, 420.55 umol, 2 eq).The mixture was stirred at 15° C. for 1 h. The resulting mixture was concentrated. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 2/1) to afford the title compound (0.09 g, 85.26 umol, 40.55% yield, 70% purity) as yellow oil.

Step 4: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1, 3, 4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (90 mg, 121.80 umol, 1 eq) in dioxane (3 mL) was added H₂SO₄ (1.19 g, 12.18 mmol, 649.26 uL, 100 eq). The mixture was stirred at 45° C. for 2 h. The mixture was adjusted pH to 8 with saturated aqueous NaOH, and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (0.12 g, crude) as a yellow solid.

Step 5: N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(5-methyl-1, 3, 4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl(2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,3, 4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.12 g, 197.16 umol, 1 eq) in DCM (3 mL) was added BBr₃ (148.18 mg, 591.49 umol, 56.99 uL, 3 eq). The mixture was stirred at 15° C. for 30 min. It was concentrated. The residue was triturated with PE/EtOAc=5/1 (5 mL) and filtered. The crude product was purified by prep-HPLC (HCl condition) to afford the title compound (19.5 mg, 38.16 umol, 19.36% yield, 100% purity, HCl) as a yellow solid.

Example 44. Synthesis of 4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 155) Step 1: Trimethyl-[2-[[6-(5-methyl-1, 3, 4-thiadiazol-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of [1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-6-yl]boronic acid (4 g, 13.69 mmol, 1 eq), 2-bromo-5-methyl-1,3,4-thiadiazole (2.45 g, 13.69 mmol, 1 eq), Cs₂CO₃ (8.92 g, 27.38 mmol, 2 eq), Pd(PPh₃)₄ (1.58 g, 1.37 mmol, 0.1 eq) in dioxane (50 mL) and H₂O (5 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. The reaction mixture was diluted with H₂O (300 mL) and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 4/1) to afford the title compound (1.6 g, 4.39 mmol, 32.04% yield, 95% purity) as a yellow solid.

Step 2: 2-[[3-bromo-6-(5-methyl-1, 3, 4-thiadiazol-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a solution of trimethyl-[2-[[6-(5-methyl-1, 3, 4-thiadiazol-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (1.6 g, 4.62 mmol, 1 eq) in DMF (20 mL) was added NBS (821.79 mg, 4.62 mmol, 1 eq). The mixture was stirred at 15° C. for 1 h. The resulting mixture was diluted with H₂O 200 mL and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 5/1) to afford the title compound (1.6 g) as a yellow solid.

Step 3: Trimethyl-[2-[[6-(5-methyl-1, 3,4-thiadiazol-2-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of 2-[[3-bromo-6-(5-methyl-1, 3, 4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane (1.6 g, 3.76 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (1.91 g, 7.52 mmol, 2 eq), AcOK (738.21 mg, 7.52 mmol, 2 eq) and Pd(dppf)Cl₂ (275.20 mg, 376.10 umol, 0.1 eq) in dioxane (30 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. It was filtered and the filtrate was concentrated. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 4:1, plate 1) to give a residue (1.5 g). 200 mg of crude product was purified by prep-HPLC (TFA condition). Then the eluent was concentrated to give a residue to afford the title compound (100 mg, TFA) as yellow oil.

Step 4: Tert-butyl(3S)-3-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

A mixture of trimethyl-[2-[[6-(5-methyl-1,3,4-thiadiazol-2-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.05 M, 3.41 mL, 1 eq, TFA), tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (77.91 mg, 204.60 umol, 1.2 eq), Na₂CO₃ (36.14 mg, 341.00 umol, 2 eq) and ditert-butyl(cyclopentyl)phosphane;dichloropalladium;iron (11.11 mg, 17.05 umol, 0.1 eq) in THF (5 mL) and H₂O (0.5 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. The reaction mixture was diluted with H₂O (50 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (60 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=10/1 to 1/1) to afford the title compound (0.11 g) as a white solid.

Step 5: 4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl(3S)-3-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.11 g, 159.22 umol, 1 eq) in dioxane (3 mL) was added H₂SO₄ (1.56 g, 15.92 mmol, 848.73 uL, 100 eq). The solution was stirred at 45° C. for 2 h. The mixture was adjusted pH to 8 with saturated aqueous NaOH, and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (HCl condition) to afford the title compound (17.4 mg, 34.89 umol, 21.91% yield, 99.65% purity, HCl) as a yellow solid.

Example 45. Synthesis of 4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 156) Step 1: 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

A mixture of 4-[1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (1.5 g, 3.59 mmol, 1 eq), 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (1.37 g, 5.38 mmol, 1.5 eq), Pd(dppf)Cl₂ (262.41 mg, 358.63 umol, 0.1 eq), KOAc (703.91 mg, 7.17 mmol, 2 eq) in dioxane (90 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. It was cooled to the room temperature and concentrated under reduced pressure to remove solvent. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=20/1 to 5/1) to afford the title compound (1.2 g) was obtained as a white solid. (Note: The reaction was combined with another reaction in 200 mg scale for purification and work up.)

Step 2: 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazol)

A mixture of 4-[1-(benzenesulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (1.1 g, 2.36 mmol, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (540.45 mg, 2.36 mmol, 1 eq), ditert-butyl(cyclopentyl) phosphane;dichloropalladium;iron (154.07 mg, 236.39 umol, 0.1 eq), Na₂CO₃ (501.10 mg, 4.73 mmol, 2 eq) in THF (40 mL) and H₂O (4 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 12 h under N₂ atmosphere. It was cooled to the room temperature and diluted with H₂O (60 mL) and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (60 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜30% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (800 mg, crude) as a yellow solid.

Step 3: 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (800 mg, 1.51 mmol, 1 eq) in EtOAc (40 mL) was added Oxone (4.63 g, 7.53 mmol, 5 eq). The mixture was stirred at 80° C. for 12 h. The reaction mixture was filtered and the filtrate was quenched by saturation Na₂SO₃ (60 mL). The water layer was extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (50 mL), dried over Na₂SO₄, filtrate and concentrated. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0˜50% Ethyl acetate/Petroleum ether gradient @ 75 mL/min) to afford the title compound (380 mg, 674.32 umol, 44.80% yield) as a pink solid.

Step 4: Benzyl(2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (170 mg, 301.67 umol, 1 eq) and benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (74.91 mg, 301.67 umol, 1 eq) in THF (2 mL) was added DIPEA (194.94 mg, 1.51 mmol, 262.72 uL, 5 eq). The mixture was stirred at 15° C. for 6 h. It was concentrated under reduced pressure to remove solvent. The residue was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash® Silica Flash Column, Eluent of 0˜25% Ethyl acetate/Petroleum ether gradient @ 50 mL/min) to afford the title compound (100 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for purification and work up.)

Step 5: Benzyl(2S,5S)-2-methyl-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl(2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (90 mg, 122.99 umol, 1 eq) in EtOH (3 mL) was added NaOH (2 M, 2.5 mL). The mixture was stirred at 60° C. for 1 h. The reaction mixture was diluted with H₂O (10 mL) and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (10 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (80 mg) as a yellow solid, and it was used into the next step without further purification. (Note: The reaction was combined with another reaction in 10 mg scale for purification and work up.)

Step 6: 4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl(2S,5S)-2-methyl-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (70 mg, 118.33 umol, 1 eq) in DCM (7 mL) was added BBr₃ (148.22 mg, 591.63 umol, 57.01 uL, 5 eq). The mixture was stirred at 15° C. for 2 h. The reaction mixture was quenched by saturation NaHCO₃ solution (1.5 mL), and then concentrated under reduced pressure to give a residue. The residue was diluted with H₂O (1.5 mL) and DMF (1.5 mL), then adjusted to pH=4 with HCl (2 N). The residue was purified by prep-HPLC (FA condition) to afford the title compound (FA, 22.2 mg, 98.26% purity) as a white solid.

Example 46. Synthesis of 4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 157) Step 1: Benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 4-[1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridin-6-yl]-3-methyl-isoxazole (170 mg, 301.67 umol, 1 eq) and benzyl (2R,5R)-5-amino-2-methyl-piperidine-1-carboxylate (74.91 mg, 301.67 umol, 1 eq) in THF (2 mL) was added DIPEA (194.94 mg, 1.51 mmol, 262.72 uL, 5 eq). The mixture was stirred at 15° C. for 6 h. The solution was concentrated under reduced pressure to remove solvent. The residue was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash® Silica Flash Column, Eluent of 0˜25% EtOAc/PE @ 50 mL/min) to afford the title compound (120 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for work up)

Step 2: Benzyl (2R,5R)-2-methyl-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-(3-methylisoxazol-4-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (110.15 mg, 150.53 umol, 1 eq) in EtOH (3 mL) was added NaOH (2 M, 2.5 mL). The mixture was stirred at 60° C. for 1 h. The reaction mixture was diluted with H₂O 10 mL and extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (10 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title (100 mg) as a yellow solid which was used into the next step without further purification.

Step 3: 4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3R,6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R,5R)-2-methyl-5-[[4-[6-(3-methylisoxazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (90 mg, 152.13 umol, 1 eq) in DCM (9 mL) was added BBr₃ (190.56 mg, 760.67 umol, 73.29 uL, 5 eq). The mixture was stirred at 15° C. for 2 h. The reaction mixture was quenched by saturation NaHCO₃ (1.5 mL), and then concentrated under reduced pressure to give a residue. The residue was diluted with H₂O (1.5 mL) and DMF (1.5 mL), then adjusted to pH=4 with HCl (2 N). The residue was purified by prep-HPLC (FA condition) to afford the title compound (FA, 20.3 mg) as a white solid.

Example 47. Synthesis of N-[(3R,6R)-6-methyl-3-piperidyl]-4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 158) Step 1: Benzyl (2R, 5R)-2-methyl-5-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(5-methyl-1,3,4-thiadiazol-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.2 g, 350.46 umol, 1 eq) in THF (2 mL) was added DIEA (135.88 mg, 1.05 mmol, 183.13 uL, 3 eq), benzyl (2R,5R)-5-amino-2-methyl-piperidine-1-carboxylate (149.68 mg, 602.79 umol, 1.72 eq). The mixture was stirred at 15° C. for 2 h. The reaction mixture was concentrated to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (250 mg) as yellow oil.

Step 2: N-[(3R,6R)-6-methyl-3-piperidyl]-4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R,5R)-2-methyl-5-[[4-[6-(5-methyl-1,3,4-thiadiazol-2-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.25 g, 338.34 umol, 1 eq) in dioxane (5 mL) was added H₂SO₄ (3.32 g, 33.83 mmol, 1.80 mL, 100 eq). The mixture was stirred at 45° C. for 2 h. The mixture was adjusted pH to 8 with saturated aqueous NaOH, and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (HCl condition) to afford the title compound (27.8 mg, 51.69 umol, 15.28% yield, 95% purity, HCl) as a yellow solid.

Example 48. Synthesis of N-[(3R,6R)-6-methyl-3-piperidyl]-4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 159) Step 1: Trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of [1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-6-yl]boronic acid (3.92 g, 13.40 mmol, 1.6 eq), 5-bromo-3-methyl-1,2,4-thiadiazole (1.5 g, 8.38 mmol, 1 eq) in dioxane (40 mL) was added K₂CO₃ (2.89 g, 20.95 mmol, 2.5 eq) and Pd(dppf)Cl₂.CH₂Cl₂ (684.19 mg, 837.81 umol, 0.1 eq) at 15° C., the reaction mixture was degassed and purged with N₂ for 3 times and stirred at 100° C. for 2 h. The resulting solution was filtered and concentrated to give a residue. The residue was purified by silica gel column (PE/EtOAc=100/1 to 25/1) to afford the title compound (1.1 g, 3.17 mmol, 37.89% yield) as a colorless oil.

Step 2: 2-[[3-bromo-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a stirred solution of trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (1.1 g, 3.17 mmol, 1 eq) in DMF (30 mL) was added NBS (553.69 mg, 3.11 mmol, 0.98 eq), the reaction mixture was stirred at 15° C. for 2 h. Then it was diluted with EtOAc (80 mL), washed with sub-saturated brine (50 mL×3) and saturated brine (50 mL). The organic layer was dried over Na₂SO₄ and concentrated to give a residue. It was purified by silica gel column (PE/EtOAc=50/1 to 20/1) to afford the title compound (1.15 g, 2.70 mmol, 85.16% yield) as a white solid.

Step 3: Trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of 2-[[3-bromo-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane (1 g, 2.35 mmol, 1 eq) and 4,4,4′,4′,5,5,5′,5′-octamethyl-2,2′-bi(1,3,2-dioxaborolane) (895.38 mg, 3.53 mmol, 1.5 eq) in dioxane (20 mL) was added KOAc (461.39 mg, 4.70 mmol, 2 eq) and Pd(dppf)Cl₂.CH₂Cl₂ (191.96 mg, 235.06 umol, 0.1 eq) at 15° C., the reaction mixture was degassed and purged with N₂ for 3 times and stirred at 100° C. for 3 h. The final reaction mixture was filtered and concentrated to give a residue. The residue was purified by silica gel column (PE/EtOAc=50/1) to afford the title compound (1.05 g, not pure) as a yellow solid. (Note: The reaction was combined with another reaction in 200 mg scale for work up.)

Step 4: Trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of trimethyl-[2-[[6-(3-methyl-1,2,4-thiadiazol-5-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (929.99 mg, 1.97 mmol, 1 eq) and 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (0.45 g, 1.97 mmol, 1 eq) in H₂O (2.5 mL) and THF (12.5 mL) was added Na₂CO₃ (417.24 mg, 3.94 mmol, 2 eq) and ditert-butyl(cyclopentyl)phosphane;dichloropalladium;iron (128.28 mg, 196.83 umol, 0.1 eq) at 15° C., the reaction mixture was degassed and purged with N₂ for 3 times, and stirred at 75° C. for 2 h. The mixture was diluted with EtOAc (50 mL), washed with H₂O (20 mL). The organic layer was dried over Na₂SO₄ and concentrated to give a residue. It was purified by silica gel column (PE/EtOAc=50/1 to 10/1) to afford the title compound (550 mg) as a white solid. (Note: The reaction was combined with another reaction in 100 mg scale for work up.)

Step 5: Trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.5 g, 928.19 umol, 1 eq) and Oxone (2.85 g, 4.64 mmol, 5 eq) in EtOAc (20 mL) was stirred at 80° C. for 12 h. It was filtered and washed with EtOAc (30 mL). The organic layer was washed with aq.Na₂SO₃ (10 mL×3), dried over Na₂SO₄ and concentrated to give a residue. The residue was purified by silica gel column (PE/EtOAc=15/1 to 5/1) to afford the title compound (120 mg) as a yellow solid.

(Note: The reaction was combined with another reaction in 50 mg scale for work up)

Step 6: Benzyl (2R,5R)-2-methyl-5-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1-(2-trimethylsilylethoxy methyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(3-methyl-1,2,4-thiadiazol-5-yl)pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.1 g, 175.23 umol, 1 eq) and benzyl (2R,5R)-5-amino-2-methylpiperidine-1-carboxylate (43.51 mg, 175.23 umol, 1 eq) in THF (2.5 mL) was added DIEA (113.24 mg, 876.14 umol, 152.61 uL, 5 eq), the reaction mixture was stirred at 20° C. for 12 h. The final reaction mixture was concentrated to give a residue. The residue was purified by silica gel column (PE/EtOAc=20/1 to 5/1) to afford the title compound (90 mg) as a yellow solid. (Note: The reaction was combined with another reaction in 20 mg scale for work up.)

Step 7: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.085 g, 115.04 umol, 1 eq) in THF (2 mL) was added TBAF (1 M, 1.73 mL, 15 eq) at 15° C., the reaction mixture was stirred at 40° C. for 4 h. It was partitioned between aq.NaHCO₃ (15 mL) and EtOAc (25 mL). The organic layer was washed with aq.NaHCO₃ (15 mL×3), dried over Na₂SO₄ and concentrated to give a residue. The residue was purified by silica gel column (PE/EtOAc=20/1 to 5/1) to afford the title compound (75 mg) of as a yellow solid. (Note: The reaction was combined with another reaction in 5 mg scale for work up.)

Step 8: N-[(3R,6R)-6-methyl-3-piperidyl]-4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R,5R)-2-methyl-5-[[4-[6-(3-methyl-1,2,4-thiadiazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (68 mg, 111.73 umol, 1 eq) in DCM (3 mL) was added BBr₃ (139.95 mg, 558.63 umol, 53.83 uL, 5 eq) at 0° C., the reaction mixture was stirred at 20° C. for 0.33 h. The resulting solution was quenched with H₂O (0.2 mL), basified to pH=7 with NaHCO₃ and concentrated. The residue was purified by HCl prep-HPLC to afford the title compound (14.3 mg, 94.3% purity) as a white solid.

Example 49. Synthesis of 4-[6-(4-methyloxazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 161) Step 1: 2-[(6-bromopyrrolo[2,3-b]pyridin-1-yl) methoxy]ethyl-trimethyl-silane

To a solution of 6-bromo-1H-pyrrolo[2,3-b]pyridine (2 g, 10.15 mmol, 1 eq) in DMF (18 mL) and THF (2 mL) was added NaH (609.04 mg, 15.23 mmol, 60% purity, 1.5 eq) at 0° C. The mixture was stirred at 0° C. for 0.5 h. Then the 2-(chloromethoxy) ethyl-trimethyl-silane (2.03 g, 12.18 mmol, 2.16 mL, 1.2 eq) was added. The resulting mixture was stirred at 15° C. for another 11.5 h. The solution was poured into H₂O (100 mL), extracted by EtOAc (50 mL×3). The combined organic layers were washed by brine (100 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (3.3 g, crude) as yellow oil, which was used into the next step without further purification.

Step 2: 1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridine-6-carbonitrile

2-[(6-bromopyrrolo[2,3-b]pyridin-1-yl) methoxy]ethyl-trimethyl-silane (0.3 g, 916.61 umol, 1 eq), 4-methyloxazole-5-carboxylic acid (233.00 mg, 1.83 mmol, 2 eq) and palladium; tritert-butylphosphane (23.42 mg, 45.83 umol, 0.05 eq), tetrabutylammonium; chloride; hydrate (271.26 mg, 916.61 umol, 1 eq), Cs₂CO₃ (447.98 mg, 1.37 mmol, 1.5 eq) were taken up into a microwave tube in DMF (9 mL). The sealed tube was heated at 170° C. for 15 min under microwave. The reaction mixture was poured into H₂O (100 mL) and extracted with EtOAc (50 mL×3). The combined organic layers were washed with brine (150 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (0.35 g, 1.06 mmol, 23.18% yield, 5 batches in parallel) as yellow oil.

Step 3: 2-[[3-bromo-6-(4-methyloxazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a solution of trimethyl-[2-[[6-(4-methyloxazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.25 g, 758.80 umol, 1 eq) in DCM (3 mL) was added NBS (81.03 mg, 455.28 umol, 0.6 eq). The mixture was stirred at 15° C. for 1 h. The solution was poured into H₂O (20 mL) and extracted with DCM (10 mL×3). The combined organic layers were washed with brine (30 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 3/1) to afford the title compound (250 mg) as yellow solid.

Step 4: trimethyl-[2-[[6-(4-methyloxazol-5-yl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of 2-[[3-bromo-6-(4-methyloxazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane (0.16 g, 391.81 umol, 1 eq) in dioxane (3.5 mL) was added BPD (149.24 mg, 587.71 umol, 1.5 eq), KOAc (76.91 mg, 783.61 umol, 2 eq) and Pd(dppf)Cl₂ (28.67 mg, 39.18 umol, 0.1 eq). The mixture was stirred at 100° C. for 1 h under N₂. It was concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (0.2 g) as yellow oil.

Step 5: Tert-butyl (3S)-3-[[4-[6-(4-methyloxazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[6-(4-methyloxazol-5-yl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.2 g, 439.15 umol, 1 eq) in THF (6 mL) and H₂O (1 mL) was added tert-butyl (3S)-3-[[4-chloro-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (167.22 mg, 439.15 umol, 1 eq), ditert-butyl(cyclopentyl) phosphane:dichloropalladium:iron (28.62 mg, 43.91 umol, 0.1 eq) and Na₂CO₃ (93.09 mg, 878.29 umol, 2 eq). The mixture was stirred at 80° C. for 2 h under N₂. The solution was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 1/1) to afford the title compound (70 mg, 68% purity) as a white solid. (Note: The reaction mixture was combined with another batch in 20 mg scale for worked up and purification.)

Step 6: 4-[6-(4-methyloxazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of tert-butyl (3S)-3-[[4-[6-(4-methyloxazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.06 g, 89.05 umol, 1 eq) in dioxane (1 mL) was added H₂SO₄ (87.34 mg, 890.47 umol, 47.47 uL, 10 eq). The mixture was stirred at 40° C. for 2 h. It was diluted with H₂O (10 mL) and adjusted pH to 12 with NaOH. Then the solution was extracted with EtOAc (10 mL×3). The combined organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (FA condition) to afford the title compound (5.5 mg, FA salt, 100% purity) as a white solid. (Note: The reaction mixture was combined with another batch in 10 mg scale for work-up and purification.)

Example 50. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 162) Step 1: 1H-pyrrolo[2,3-b]pyridine-6-carbonitrile

A mixture of 6-bromo-1H-pyrrolo[2,3-b]pyridine (10 g, 50.75 mmol, 1 eq), Zn (331.88 mg, 5.08 mmol, 0.1 eq), Zn(CN)₂ (4.17 g, 35.53 mmol, 2.26 mL, 0.7 eq) and Pd(dppf)Cl₂.CH₂Cl₂ (2.07 g, 2.54 mmol, 0.05 eq) in DMF (100 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 140° C. for 5 h under N₂ atmosphere. It was diluted with water (500 mL) and EtOAc (300 mL), and then filtered to remove the solid, the solid was washed with EtOAc (200 mL×2). The combined organic layers were washed with brine (500 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=5/1 to 2/1) to afford the title compound (5.3 g, 89% purity) as a green solid.

Step 2: 3-bromo-1H-pyrrolo[2,3-b]pyridine-6-carbonitrile

To a solution of 1H-pyrrolo[2,3-b]pyridine-6-carbonitrile (4 g, 25.15 mmol, 1 eq) in DCM (40 mL) was added NBS (5.37 g, 30.18 mmol, 1.2 eq) at 0° C. The mixture was stirred at 15° C. for 1 h. It was concentrated and the residue was washed with PE (500 mL) and the solid was filtered to afford the title compound (5 g, crude) as a yellow solid.

Step 3: 1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridine-6-carbonitrile

To a solution of 3-bromo-1H-pyrrolo[2,3-b]pyridine-6-carbonitrile (5 g, 22.52 mmol, 1 eq) in THF (50 mL) was added NaH (900.65 mg, 22.52 mmol, 60% purity, 1 eq) at 0° C. The mixture was stirred at 0° C. for 0.5 h. And then benzenesulfonyl chloride (5.17 g, 29.27 mmol, 3.75 mL, 1.3 eq) was added into the mixture was stirred at 15° C. for 1 h. It was quenched by addition water (200 mL) at 15° C., and then extracted with EtOAc (100 mL×2). The combined organic layers were washed with brine (200 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=7/1 to 2/1) to afford a crude product (4.5 g). Then it was triturated with EtOAc (5 mL) and PE (50 mL), the solid was filtered and dried to afford the title compound (4 g, 95% purity) as a white solid.

Step 4: 1-(benzenesulfonyl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridine-6-carbonitrile

A mixture of 1-(benzenesulfonyl)-3-bromo-pyrrolo[2,3-b]pyridine-6-carbonitrile (4 g, 11.04 mmol, 1 eq), BPD (4.21 g, 16.57 mmol, 1.5 eq), KOAc (2.17 g, 22.09 mmol, 2 eq), Pd(dppf)Cl₂ (1.21 g, 1.66 mmol, 0.15 eq) in dioxane (40 mL) was degassed and purged with N₂ for 5 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. It was filtered, and washed by EtOAc (200 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was combined with the solid and purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=6/1 to 3/1) to afford the title compound (4 g, 85% purity) as an orange solid.

Step 5: 1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridine-6-carbonitrile

A mixture of 1-(benzenesulfonyl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl)pyrrolo[2,3-b]pyridine-6-carbonitrile (2 g, 4.89 mmol, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (1.68 g, 7.33 mmol, 1.5 eq), ditert-butyl (cyclopentyl) phosphane:dichloropalladium:iron (318.50 mg, 488.68 umol, 0.1 eq), Na₂CO₃ (1.04 g, 9.77 mmol, 2 eq) in THF (60 mL) and H₂O (6 mL) was degassed and purged with N₂ for 5 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. It was filtered to remove the solid, and washed with EtOAc (250 mL×2). The filtrate was washed with brine (500 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=6/1 to 2/1) to afford the title compound (0.8 g) as a white solid. (Note: The reaction was combined with another reaction in 100 mg scale for work-up.)

Step 6: 1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridine-6-carbonitrile

To a solution of 1-(benzenesulfonyl)-3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridine-6-carbonitrile (0.06 g, 115.05 umol, 1 eq, FA) in DCM (4 mL) was added m-CPBA (51.39 mg, 253.12 umol, 85% purity, 2.2 eq) and Na₂SO₄ (18.23 mg, 128.38 umol, 13.02 uL, 1.12 eq). The mixture was stirred at 15° C. for 2 h. The reaction mixture was poured into the saturated Na₂SO₃ and NaHCO₃ solution (200 mL), then extracted with DCM (100 mL×3), the combined organic layers were washed with brine (300 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (900 mg, crude) as a white solid which was used directly into the next step without purification. (Note: The reaction was combined with another reaction in 800 mg scale for work-up.)

Step 7: Benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-cyano-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridine-6-carbonitrile (0.42 g, 827.64 umol, 1 eq) in THF (4.6 mL) was added DIPEA (213.93 mg, 1.66 mmol, 288.31 uL, 2 eq) and benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (246.62 mg, 993.17 umol, 1.2 eq). The mixture was stirred at 15° C. for 1 h. It was concentrated under reduced pressure to remove solvent. The residue was diluted with water (20 mL) and extracted with EtOAc (20 mL×2). The combined organic layers were washed with brine (40 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=4/1 to 2/1) to afford the title compound (300 mg, 80% purity) as a white solid. (Note. The reaction was combined with another reaction in 40 mg scale for work-up.)

Step 8: Benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-[(E)-N′-hydroxycarbamimidoyl]pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-cyano-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (300.00 mg, 444.00 umol, 1 eq) in EtOH (20 mL) was added hydroxylamine; hydrochloride (308.54 mg, 4.44 mmol, 10 eq) and Na₂CO₃ (564.71 mg, 5.33 mmol, 12 eq). The mixture was stirred at 30° C. for 16 h. It was filtered, and the filtrate was concentrated under reduced pressure to afford the title compound (400 mg, crude) as a white solid which was used directly into the next step without purification.

Step 9: Benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1, 2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

Benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-[(E)-N′-hydroxycarbamimidoyl]pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.36 g, 507.97 umol, 1 eq) in 1, 1, 1-triethoxyethane (0.4 mL) was added TFA (2.90 mg, 25.40 umol, 1.88 uL, 0.05 eq). The mixture was stirred at 15° C. for 10 min. Then the mixture was stirred at 60° C. for 30 min. The solution was concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=2/1) to afford the title compound (220 mg, 96% purity) as a white solid.

Step 10: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-5-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1,2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.2 g, 272.95 umol, 1 eq) in MeOH (24 mL) was added NaOH (2 M, 4.09 mL, 30 eq). The mixture was stirred at 60° C. for 0.5 h. The reaction mixture was concentrated under reduced pressure to remove solvent. It was diluted with water 30 mL, adjusted pH to 7 by added HCl (1 M), and then extracted with EtOAc (30 mL). The organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (180 mg, crude) as a white solid. The crude product was used directly into the next step without purification. (Note: The reaction was combined with another reaction in 20 mg scale for work-up.)

Step 11: 4-[6-(5-methyl-1, 2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (160 mg, 270.01 umol, 1 eq) in DCM (3.2 mL) was added BBr₃ (676.43 mg, 2.70 mmol, 260.17 uL, 10 eq) at 0° C., and then the mixture was stirred at this temperature for 1 h. It was concentrated under reduced pressure to give a residue, and then it was washed with PE (160 mL) and collected the cake. The crude product was purified by prep-HPLC (FA condition) to afford the title compound (26.7 mg, FA, 100% purity, 100% ee value) as a white solid. (Note: The reaction was combined with another reaction in 20 mg scale for work-up.)

Example 51. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3R, 6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 163) Step 1: Benzyl (2R, 5R)-5-[[4-[1-(benzenesulfonyl)-6-cyano-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 1-(benzenesulfonyl)-3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]pyrrolo[2,3-b]pyridine-6-carbonitrile (400 mg, 788.23 umol, 1 eq) in THF (4 mL) was added DIPEA (203.75 mg, 1.58 mmol, 274.59 uL, 2 eq) and benzyl (2R, 5R)-5-amino-2-methyl-piperidine-1-carboxylate (234.88 mg, 945.88 umol, 1.2 eq). The mixture was stirred at 15° C. for 1 h. It was concentrated under reduced pressure to remove solvent. The residue was diluted with water 20 mL and extracted with EtOAc (20 mL×2). The combined organic layers were washed with brine (40 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=4/1 to 2/1) to afford the title compound (350 mg, 70% purity) as a white solid.

Step 2: Benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-[(E)-N′-hydroxycarbamimidoyl]pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl (2R,5R)-5-[[4-[1-(benzenesulfonyl)-6-cyano-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (350.00 mg, 518.00 umol, 1 eq) in EtOH (23 mL) was added hydroxylamine; hydrochloride (359.96 mg, 5.18 mmol, 10 eq) and Na₂CO₃ (658.82 mg, 6.22 mmol, 12 eq). The mixture was stirred at 30° C. for 16 h. It was filtered, and the filtrate was concentrated under reduced pressure to afford the title compound (400 mg, crude) as a white solid which was used directly into the next step without purification.

Step 3: Benzyl (2R, 5R)-5-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1,2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of benzyl (2R, 5R)-5-[[4-[1-(benzenesulfonyl)-6-[(E)-N′-hydroxycarbamimidoyl]pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (400.00 mg, 564.41 umol, 1 eq) in AcOH (4 mL) was added Ac₂O (69.14 mg, 677.29 umol, 63.44 uL, 1.2 eq). The mixture was stirred at 90° C. for 16 h. It was residue was diluted with water 30 mL. The solid was formed and filtered to collect the cake. The crude product was purified by column chromatography (SiO₂, Petroleum ether/Ethyl acetate=5/1 to 3/1) to afford the title compound (180 mg, 94% purity) as a white solid.

Step 4: Benzyl (2R, 5R)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2R, 5R)-5-[[4-[1-(benzenesulfonyl)-6-(5-methyl-1,2,4-oxadiazol-3-yl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (0.1 g, 136.48 umol, 1 eq) in MeOH (12 mL) was added NaOH (2 M, 2.05 mL, 30 eq). The mixture was stirred at 60° C. for 0.5 h. It was concentrated under reduced pressure to remove solvent. The residue was diluted with water 30 mL, adjusted pH to 7 by added HCl (1 M), and then extracted with EtOAc (30 mL). The organic layers were washed with brine (30 mL), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (110 mg, crude) as a white solid. The crude product was used directly into the next step without purification. (Note: The reaction was combined with another reaction in 20 mg scale for work-up and purification.)

Step 5: 4-[6-(5-methyl-1, 2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-N-[(3R, 6R)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R, 5R)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (80 mg, 135.01 umol, 1 eq) in DCM (1.6 mL) was added BBr₃ (338.22 mg, 1.35 mmol, 130.08 uL, 10 eq) at 0° C., and then the mixture was stirred at this temperature for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue, and then the residue was triturated with PE (60 mL), filtered and dried. The crude product was purified by prep-HPLC (FA condition) to afford the title compound (17.3 mg, FA, 100% purity, 100% ee value) as a white solid. (Note: The reaction mixture was combined with another batch in 15 mg scale for worked up and purification.)

Example 52. Synthesis of N-[(3R, 6R)-6-methyl-3-piperidyl]-4-[6-(1-methyltetrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 164) Step 1: Benzyl (2R, 5R)-2-methyl-5-[[4-[6-(1-methyltetrazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.27 g, 486.82 umol, 1 eq), benzyl (2R, 5R)-5-amino-2-methyl-piperidine-1-carboxylate (181.33 mg, 730.23 umol, 1.5 eq) in THF (5 mL) was added DIEA (188.75 mg, 1.46 mmol, 254.38 uL, 3 eq). The mixture was stirred at 20° C. for 2 h. The reaction mixture was concentrated to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (0.22 g, 295.23 umol, 60.64% yield, 97% purity) as a yellow solid.

Step 2: N-[(3R, 6R)-6-methyl-3-piperidyl]-4-[6-(1-methyltetrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2R, 5R)-2-methyl-5-[[4-[6-(1-methyltetrazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.22 g, 304.36 umol, 1 eq) in dioxane (5 mL) was added H₂SO₄ (4.48 g, 45.65 mmol, 2.43 mL, 150 eq). The mixture was stirred at 45° C. for 2 h. The mixture was adjusted pH to 8 with saturated aqueous NaOH, and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (FA condition) to afford the title compound (31.4 mg, 56.64 umol, 18.610% yield, 910% purity, FA) as a white solid.

Example 53. Synthesis of N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(1-methyltetrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 165) Step 1: 5-iodo-1-methyl-tetrazole

To a solution of 1-methyltetrazole (3 g, 35.68 mmol, 1 eq) in THF (90 mL) was added dropwise n-BuLi (2.5 M, 18.55 mL, 1.3 eq) at −78° C. under N₂ atmosphere. After addition, the mixture was stirred at this temperature for 30 min, and then molecular iodine (9.06 g, 35.68 mmol, 7.19 mL, 1 eq) was added at −78° C. The resulting mixture was stirred at 15° C. for 1 h. The mixture was diluted with H₂O (200 mL) and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄ filtered and concentrated under reduced pressure to afford the title compound (3 g, crude) as brown oil.

Step 2: Trimethyl-[2-[[6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of [1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-6-yl]boronic acid (3.96 g, 13.55 mmol, 1 eq), 5-iodo-1-methyl-tetrazole (3.7 g, 17.62 mmol, 1.3 eq), Cs₂CO₃ (8.83 g, 27.11 mmol, 2 eq), Pd(PPh₃)₄ (1.57 g, 1.36 mmol, 0.1 eq) in dioxane (70 mL) and H₂O (7 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 1 h under N₂ atmosphere. It was diluted with H₂O 300 mL and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue that was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 4/1) to afford the title compound (2 g) as a yellow solid. (Note: The reaction was combined with another reaction in 500 mg scale for work up.)

Step 3: 2-[[3-bromo-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane

To a solution of trimethyl-[2-[[6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (1.7 g, 5.14 mmol, 1 eq) in DMF (40 mL) was added NBS (915.59 mg, 5.14 mmol, 1 eq). The mixture was stirred at 15° C. for 1 h. The mixture was diluted with H₂O 200 mL and extracted with EtOAc (100 mL×3). The combined organic layers were washed with brine (300 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. It was washed with MTBE (8 mL) and filtered to afford the title compound (1.9 g) as a red solid. (Note: The reaction was combined with another reaction in 300 mg scale for work up.)

Step 4: Trimethyl-[2-[[6-(1-methyltetrazol-5-yl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of 2-[[3-bromo-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl-trimethyl-silane (1.8 g, 4.40 mmol, 1 eq), 4, 4, 5, 5-tetramethyl-2-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl)-1, 3, 2-dioxaborolane (2.23 g, 8.79 mmol, 2 eq), AcOK (863.07 mg, 8.79 mmol, 2 eq) and Pd(dppf)Cl₂ (321.74 mg, 439.72 umol, 0.1 eq) in dioxane (40 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 100° C. for 2 h under N₂ atmosphere. The solution was filtered and the filtrate was concentrated to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 5/1) to give a residue. Then the residue was purified by reverse column. The eluent solution was adjusted pH to 8 with NaHCO₃ and extracted with EtOAc (60 mL×3), The combined organic layers were washed with brine (200 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to afford the title compound (700 mg) as a white solid.

Step 5: Trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

A mixture of trimethyl-[2-[[6-(1-methyltetrazol-5-yl)-3-(4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaborolan-2-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.05 M, 28.48 mL, 1 eq), 4-chloro-2-methylsulfanyl-5-(trifluoromethyl)pyrimidine (488.38 mg, 2.14 mmol, 1.5 eq), Na₂CO₃ (301.89 mg, 2.85 mmol, 2 eq) and ditert-butyl (cyclopentyl) phosphane:dichloropalladium:iron (92.82 mg, 142.41 umol, 0.1 eq) in THF (30 mL) and H₂O (3 mL) was degassed and purged with N₂ for 3 times, and then the mixture was stirred at 80° C. for 1 h under N₂ atmosphere. It was diluted with H₂O 80 mL and extracted with EtOAc (30 mL×3). The combined organic layers were washed with brine (60 mL×2), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 5/1) to afford the title compound (660 mg) as yellow oil. (Note: The reaction was combined with another reaction in 50 mg scale for work up.)

Step 6: Trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane

To a solution of trimethyl-[2-[[3-[2-methylsulfanyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.66 g, 1.26 mmol, 1 eq) in DCM (10 mL) was added m-CPBA (640.98 mg, 3.16 mmol, 85% purity, 2.5 eq). The mixture was stirred at 15° C. for 3 h. The mixture was washed with Sat.Na₂SO₃ (30 mL), Sat.NaHCO₃ (30 mL), brine (50 mL). The organic layers were dried over Na₂SO₄ and concentrated to give a residue. The residue was washed with PE/EtOAc=5/1 (8 mL) and filtered to afford the title compound (0.54 g, crude) as a yellow solid.

Step 7: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(1-methyltetrazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of trimethyl-[2-[[3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-6-(1-methyltetrazol-5-yl) pyrrolo[2,3-b]pyridin-1-yl]methoxy]ethyl]silane (0.27 g, 486.82 umol, 1 eq), benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (145.06 mg, 584.18 umol, 1.2 eq) in THF (5 mL) was added DIEA (188.75 mg, 1.46 mmol, 254.38 uL, 3 eq). The mixture was stirred at 20° C. for 2 h. The resulting solution was concentrated to give a residue. It was purified by column chromatography (SiO₂, PE/EtOAc=10/1 to 2/1) to afford the title compound (0.26 g, 348.90 umol, 71.67% yield, 97% purity) as a yellow solid.

Step 8: N-[(3S,6S)-6-methyl-3-piperidyl]-4-[6-(1-methyltetrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(1-methyltetrazol-5-yl)-1-(2-trimethylsilylethoxymethyl)pyrrolo[2,3-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (0.25 g, 345.86 umol, 1 eq) in dioxane (5 mL) was added H₂SO₄ (5.09 g, 51.88 mmol, 2.77 mL, 150 eq). The mixture was stirred at 45° C. for 2 h. The solution was adjusted pH to 8 with saturated aqueous NaOH, and extracted with EtOAc (50 mL×3), dried over Na₂SO₄, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (FA condition) to afford the title compound (30.9 mg, FA) as a white solid. (Note: The reaction was combined with another reaction in 10 mg scale for purification).

Example 54. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 167) Step 1: Benzyl (2S,5S)-5-[[4-(6-cyano-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a solution of 3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridine-6-carbonitrile (150 mg, 331.56 umol, 1 eq) in THF (2 mL) was added benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (98.80 mg, 397.87 umol, 1.2 eq) and DIEA (428.52 mg, 3.32 mmol, 577.51 uL, 10 eq). The mixture was stirred at 15° C. for 1 h. It was poured into water (5 mL) and extracted with EtOAc (10 mL×3). The combined organic layer was washed with brine (10 mL×3) and sat. NaHCO₃ (20 mL), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. The residue was purified by MPLC (SiO₂, PE/EtOAc=3/1 to 1/1) to afford the title compound (85 mg, crude) as white solid.

Step 2: Benzyl (2S,5S)-5-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate

To a mixture of benzyl (2S,5S)-5-[[4-(6-cyano-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (85.00 mg, 136.96 umol, 1 eq) in EtOH (2 mL) was added Na₂CO₃ (174.19 mg, 1.64 mmol, 12 eq) and NH₂OH.HCl (95.17 mg, 1.37 mmol, 10 eq). The mixture was stirred at 30° C. for 12 h. It was 10 filtered and concentrated under reduced pressure to afford the title compound (100 mg, crude) as yellow solid which was used next step without further purification. (Note: The reaction was combined with another reaction in 200 mg scale for work up.)

Step 3: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-5-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-methyl-piperidine-1-carboxylate (100 mg, 152.99 umol, 1 eq) in 1, 1, 1-triethoxyethane (885.00 mg, 5.46 mmol, 1 mL, 35.66 eq) was added TFA (3.49 mg, 30.60 umol, 2.27 uL, 0.2 eq) at 15° C. The mixture was stirred at 15° C. for 10 min, then the mixture was stirred at 60° C. for 50 min. The mixture was concentrated to obtain the residue. It was purified by MPLC (SiO₂, PE/EtOAc=5/1 to 1/1) to afford the title compound (50 mg, 67.51 umol, 44.13% yield, 91.5% purity) as brown solid.

Step 4: Benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (50.00 mg, 73.78 umol, 1 eq) in HCl/MeOH (2 mL) was stirred at 60° C. for 12 h. The reaction mixture was concentrated under reduced pressure to afford the title compound (50 mg, crude) as yellow solid.

Step 5: 4-[6-(5-methyl-1, 2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S,6S)-6-methyl-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of benzyl (2S,5S)-2-methyl-5-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (50.00 mg, 84.24 umol, 1 eq) in DCM (2 mL) was added BBr₃ (105.52 mg, 421.19 umol, 40.58 uL, 5 eq) at 0° C. The mixture was stirred at 0° C. for 1 h. The reaction mixture was concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (HCl condition) to afford the title compound (12.7 mg, 23.76 umol, 28.21% yield, 92.78% purity, HCl) as white solid.

Example 55. Synthesis of 4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine (Compound 168) Step 1: Tert-butyl (3S)-3-[[4-(6-cyano-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of 3-[2-methylsulfonyl-5-(trifluoromethyl)pyrimidin-4-yl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridine-6-carbonitrile (160 mg, 353.66 umol, 1 eq) in THF (1.6 mL) was added tert-butyl (3S)-3-aminopiperidine-1-carboxylate (77.91 mg, 389.03 umol, 1.1 eq), DIEA (228.54 mg, 1.77 mmol, 308.01 uL, 5 eq) at 15° C. The mixture was stirred at 15° C. for 1 h. It was poured into water (10 mL) and extracted with EtOAc (10 mL×3). The combined organic layer was washed with brine (10 mL×3), dried over Na₂SO₄, filtered. The filtrate was concentrated under reduced pressure to give a residue. It was purified by MPLC (SiO₂, PE/EtOAc=3/1 to 1/1) to afford the title compound (200 mg) as yellow solid.

Step 2: Tert-butyl (3S)-3-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a solution of tert-butyl (3S)-3-[[4-(6-cyano-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (200 mg, 349.30 umol, 1 eq) in EtOH (5 mL) was added NH₂OH.HCl (242.73 mg, 3.49 mmol, 10 eq) and Na₂CO₃ (444.26 mg, 4.19 mmol, 12 eq). The mixture was stirred at 30° C. for 12 h. It was filtered and concentrated under reduced pressure to afford the title compound (200 mg, crude) as yellow solid which was used next step directly. (Note: The reaction was combined with another reaction in 200 mg scale for work up.)

Step 3: Tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate

To a mixture of tert-butyl (3S)-3-[[4-[6-[(Z)—N′-hydroxycarbamimidoyl]-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (180 mg, 297.22 umol, 1 eq) and 1, 1, 1-triethoxyethane (964.36 mg, 5.94 mmol, 1.09 mL, 20 eq) was added TFA (3.39 mg, 29.72 umol, 2.20 uL, 0.1 eq). The mixture was stirred at 15° C. for 10 min, and then the mixture was stirred at 60° C. for 50 min. It was concentrated. The residue was purified by MPLC (SiO₂, PE/EtOAc=4/1 to 1/1) to afford the title compound (100 mg, 93.7% purity) as white solid.

Step 4: 4-[6-(5-methyl-1, 2,4-oxadiazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-N-[(3S)-3-piperidyl]-5-(trifluoromethyl)pyrimidin-2-amine

A solution of tert-butyl (3S)-3-[[4-[6-(5-methyl-1,2,4-oxadiazol-3-yl)-1-tetrahydropyran-2-yl-pyrazolo[3,4-b]pyridin-3-yl]-5-(trifluoromethyl)pyrimidin-2-yl]amino]piperidine-1-carboxylate (100 mg, 158.82 umol, 1 eq) in HCl/MeOH (3 mL) was stirred at 60° C. for 12 h. It was concentrated under reduced pressure to give a residue. It was purified by prep-HPLC (HCl condition) to afford the title compound (42 mg, 86.40 umol, 54.40% yield, 99.13% purity, HCl) as white solid.

Example 56. Synthesis of 4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-indol-3-yl)-N—((S)-piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 134) Step 1: 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-5-fluoro-1H-indole

To a andrt solution of 2,4-dichloro-5-trifluoromethylpyrimidine (945 uL, 7.01 mmol) in anh. (anhydrous) DCE (3 mL) under nitrogen, was added aluminum trichloride (472 mg, 3.51 mmol), and the resulting mixture was stirred at 80° C. for 30 min. After this time, the reaction mixture was cooled to RT, and 6-bromo-5-fluoro indole (500 mg, 2.34 mmol) was added. The resulting mixture was stirred at 80° C. for 3 h, where the solution became reddish overtime. The mixture was then poured into crushed ice and EtOAc. Layers were separated, and organic layer was then dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by reverse phase chromatography (C18, ACN in aq. 10 mM ammonium formate, pH 3.8, 45 to 85% gradient) to afford the title compound (431 mg, 1.09 mmol, 47% yield) as a beige solid.

Step 2: (S)-tert-butyl 3-((4-(6-bromo-5-fluoro-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of 6-bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-5-fluoro-1H-indole (410 mg, 1.04 mmol) and (S)-tert-butyl 3-aminopiperidine-1-carboxylate (234 mg, 1.14 mmol) in anh. NMP (2.1 mL), was added DIPEA (0.55 mL, 3.12 mmol). The reaction mixture was stirred at 70° C. for 16 h. The mixture was then diluted with EtOAc, washed with brine (2×20 mL), dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by column chromatography on silica gel (EtOAc in hexanes, 0 to 100% gradient) to afford the title compound (355 mg, 0.635 mmol, 61% yield) as a pale yellow oil that crystallized overtime.

Step 3: (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

(S)-tert-Butyl 3-((4-(6-bromo-5-fluoro-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (100 mg, 0.179 mmol) and 3,5-dimethyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)isoxazole (80 mg, 0.358 mmol) were dissolved in a previously degassed mixture of dioxane (3.0 mL) and water (1.5 mL). Cesium carbonate (118 mg, 0.358 mmol) and Pd(PPh₃)₄ (21 mg, 0.018 mmol) were then added to the reaction mixture subsequently. The resulting mixture was stirred at 100° C. for 3 h. After full conversion of starting material, the mixture was cooled to RT, diluted with water, and extracted with EtOAc (3×20 mL). Organic layers were combined, dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by column chromatography on silica gel (EtOAc in Hexanes, 0 to 100% gradient) to provide the title compound (88 mg, 0.153 mmol, 86% yield) as a pale yellow oil.

Step 4: 4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-indol-3-yl)-N—((S)-piperidin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (88 mg, 0.153 mmol) in DCM (2.25 mL), was added TFA (0.6 mL, 7.67 mmol). After 1 h of stirring at RT, the reaction mixture was concentrated to dryness in vacuo. The crude was then re-dissolved in MeTHF and washed twice with aq. sat. NaHCO₃. Organic layer was concentrated, and the obtained residue was purified by reverse phase chromatography (C18, ACN in aq. 10 mM ammonium formate, pH 3.8, 0 to 55% gradient) to afford the title compound (29.6 mg, 0.062 mmol, 41% yield) as a white solid after lyophilization.

Example 57. Synthesis of (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (Compound 138) Step 1: 4-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

6-Bromo-5-fluoro-1H-pyrrolo[2,3-b]pyridine (592 mg, 2.67 mmol) and 3,5-dimethylisoxazol-4-yl-4-boronic acid (792 mg, 5.34 mmol) were dissolved in degassed 2:1 mixture of dioxane and water (30/15 mL). Cesium carbonate (1.75 g, 5.34 mmol) was added, and the mixture was degassed for 5 min. Pd(Ph₃)₄ (312 mg, 267 umol) was then added, and the reaction mixture was stirred at 100° C. for 3 h. The mixture was cooled to RT and diluted with water, the crude product was extracted from aq. phase with MeTHF (3 times). Organics were combined, dried over anh. Na₂SO₄, filtered, and concentrated in vacuo. The residue was purified by silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient) to afford the title compound (500 mg, 2.16 mmol, 81% yield) as a yellowish solid.

Step 2: 4-(3-bromo-5-fluoro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

To a solution of 4-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (500 mg, 2.16 m mol) in DCM (22 mL), was added NBS (388 mg, 2.16 mmol), and the reaction mixture was stirred at RT for 16 h. The mixture was quenched by the addition of Na₂S₂O₃ (aq. sat.) and stirred vigorously for 30 min. DCM was concentrated, and the crude product was extracted from aq. phase with EtOAc (3×30 mL). The combined organic phase was again washed with aq. sat. NaS₂SO₃ (20 mL), water (2×10 mL), brine (2×20 mL), then dried over anh. Na₂SO₄, filtered, and concentrated in vacuo to afford the title compound as an orange-brown solid (666 mg, 2.15 mmol, quant. yield), which was used in the next step without further purification.

Step 3: 4-(3-bromo-5-fluoro-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

A solution of 4-(3-bromo-5-fluoro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (666 mg, 2.15 mmol) in THF (21.5 mL) was cooled to 0° C. and then treated with sodium tert-butoxide (248 mg, 2.58 mmol). After stirring for 30 min at this temperature, benzenesulfonyl chloride (303 uL, 2.25 mmol) was added, and the reaction mixture was stirred at RT until full conversion. The mixture was poured into water (50 mL), and then THF was concentrated under reduced pressure. The formed solid was filtered, washed with water, and dried in vacuo to afford the title compound as a tan solid (919 mg, 2.04 mmol, 95% yield), which was used in the next step without further purification.

Step 4: 4-(5-fluoro-1-(phenylsulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole

A mixture of 4-(3-bromo-5-fluoro-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (455 mg, 1.01 mmol), potassium acetate (501 mg, 5.05 mmol) and B₂Pin₂ (bis(pinacolato)diboron; 655 mg, 2.53 mmol) in dioxane (10 mL) was degassed for 30 min by bubbling with nitrogen. Pd(dppf)Cl₂ (37.5 mg, 50.5 umol) was then added, and the reaction mixture was stirred in a sealed vial at 100° C. until full conversion (30 min). The mixture was cooled to RT, diluted with EtOAc, and filtered through Celite pad. The organic phase was washed with water (2×10 mL), brine (2×10 mL), dried over anh. Na₂SO₄, and concentrated in vacuo to afford the title compound as a yellowish oil (503 mg, 1.01 mmol, quant. yield), which was used in the next step without further purification.

Step 5: (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

A solution of 4-(5-fluoro-1-(phenylsulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3,5-dimethylisoxazole (503 mg, 1.01 mmol), (S)-tert-butyl 3-((4-chloro-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate [prepared as in PCT/US2014/015256] (424 mg, 1.11 mmol) and cesium carbonate (664 mg, 2.02 mmol) in dioxane and water (20 mL/10 mL) was degassed for 30 min by bubbling with nitrogen. Pd(PPh₃)₄ (119 mg, 0.101 mmol) was then added, and the reaction mixture was stirred at 100° C. for 2 h. The mixture was cooled to RT and concentrated under reduced pressure to remove dioxane. After re-dissolving in EtOAc (30 mL) and water (15 mL), the aqueous layer was extracted with EtOAc (2×15 mL). The collected organic phase was washed with water (2×15 mL), brine (2×15 mL), dried over anh. Na₂SO₄, filtered, and concentrated. The residue was purified by flash silica gel column chromatography (EtOAc in hexanes, 0 to 100% gradient) to provide the title compound (410 mg, 0.573 mmol, 57% yield) as a pale yellow solid.

Step 6: (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

To a solution of (3S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-5-fluoro-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (410 mg, 0.573 mmol) in dioxane (5 mL), was added aq. 5 M solution of sodium hydroxide (2.29 mL, 11.5 mmol), and the reaction mixture was stirred at 70° C. until full conversion (30 min). Cooled to RT, the mixture was concentrated, then re-dissolved in MeTHF, and water (20 mL) was added. The mixture was acidified to pH 3 with aq. 1 M HCl, then aq. layer was extracted with MeTHF (2×15 mL). The combined organic phase was washed with water (2×15 mL), brine (2×15 mL), dried over anh. Na₂SO₄, filtered, and concentrated in vacuo to afford the title compound (319 mg, 0.554 mmol, 97% yield) as a pale yellow solid, which was used in the next step without further purification.

Example 58. Synthesis of (S)-tert-butyl 3-((4-(6-(3,5-dimethylisothiazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (Compound 166) Step 1: (S)-3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-1H-pyrrolo[2,3-b]pyridine 7-oxide

To a suspension of (S)-tert-butyl 3-((4-(1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate [prepared from 1-(phenylsulfonyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine and (S)-tert-butyl 3-((4-chloro-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate as in Example 57] (3.20 g, 6.92 mmol) in DCM (68 mL) at 0° C., was added m-CPBA, 77%, portion wise (4.65 g, 20.76 mmol, 3 eq in total) over 16 h, stirring the reaction mixture at RT and monitoring conversion by LCMS. Then, water (50 mL) was added, and the crude product was extracted with DCM (2×100 mL). The combined organic phase was washed with sat. aq. NaHCO₃ (50 mL), brine (2×50 mL), dried over anh. Na₂SO₄, filtered, and concentrated in vacuo. The residue was purified by reverse phase column chromatography (C18, ACN in aq. 10 mM ammonium formate, pH 3.8, 0 to 100% gradient) to afford the title compound (1.2 g, 2.5 mmol, 36% yield) as a red solid.

Step 2: (S)-Methyl 3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-6-chloro-1H-pyrrolo[2,3-b]pyridine-1-carboxylate

To a suspension of (S)-3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-1H-pyrrolo[2,3-b]pyridine 7-oxide (1.09 g, 2.27 mmol) in THF (12 mL), was added HMDS (1,1,1,3,3,3-Hexamethyldisilazane; 517 uL, 2.50 mmol), and the mixture was stirred under nitrogen at 0° C. Then, methyl chloroformate (443 uL, 5.68 mmol) was added, and the reaction mixture was stirred at RT until full conversion (4 h). The mixture was diluted with EtOAc, washed with aq. sat. NaHCO₃, water and brine, then dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by flash column silica gel chromatography (EtOAc in hexanes, 0 to 100% gradient) to provide the title compound (567 mg, 1.02 mmol, 45% yield) as a yellow foam.

Step 3: (S)-tert-butyl 3-((4-(6-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

(S)-Methyl 3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-6-chloro-1H-pyrrolo[2,3-b]pyridine-1-carboxylate (567 mg, 1.02 mmol) was dissolved in THF (5 mL), and 2 M aq. sodium hydroxide (1 mL, 2.04 mmol) was added. The reaction mixture was stirred at RT until full conversion (1 h). The mixture was then diluted with MeTHF and water, and the organic layer was separated. The organic phase was dried over anh. Na₂SO₄, filtered, and concentrated in vacuo to afford the title compound (507 mg, quant. yield), which was used in the next step without further purification.

Step 4: (S)-(3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)boronic acid

A flask was charged with (S)-tert-butyl 3-((4-(6-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate (507 mg, 1.02 mmol), bis(pinacolato)diboron (317 mg, 1.22 mmol), potassium acetate (506 mg, 5.10 mmol), and degassed dioxane (13 mL). The mixture was degassed for another 5 min, and then Pd(dppf)Cl₂×DCM complex (85 mg, 102 umol) was added. The reaction mixture was stirred at 100° C. for 16 h. The reaction mixture was cooled to RT, diluted with EtOAc, and filtered through Celite pad. The organic phase was washed with water and brine, dried over anh. Na₂SO₄, and concentrated in vacuo. The obtained dark-brown crude was triturated with the mixture of hexane/ether to afford the title compound as a grey solid, which was used in the next step without further purification.

Step 5: (S)-tert-butyl 3-((4-(6-(3,5-dimethylisothiazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)piperidine-1-carboxylate

(S)-(3-(2-((1-(tert-butoxycarbonyl)piperidin-3-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)boronic acid (crude from the previous step, 1.02 mmol) and 4-bromo-3,5-dimethylisothiazole (274 mg, 1.43 mmol) were dissolved in degassed 2:1 mixture of dioxane and water (14/7 mL). Cesium carbonate (669 mg, 2.04 mmol) was added, and after degassing for 5 min, Pd(PPh₃)₄ (120 mg, 102 umol) was added. The reaction mixture was stirred at 100° C. for 1 h. Reaction mixture was cooled to RT and diluted with water, the product was extracted 2 times with EtOAc. Organics were combined, dried over anh. Na₂SO₄, filtered, and concentrated. Residue was purified by reverse phase chromatography (C18, ACN in aq. 10 mM ammonium formate, pH 3.8, 0 to 100% gradient) to provide the title compound (132 mg, 0.23 mmol, 22% yield over 2 steps) as a brown foam.

Example 59. Synthesis of (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(6-(3-methylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (Compound 160) Step 1: 3-methyl-4-(1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole

A mixture of 6-chloro-1H-pyrazolo[3,4-b]pyridine (565 mg, 3.68 mmol), 3-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)isoxazole (1.10 g, 5.15 mmol), Pd(dppf)Cl₂ (150 mg, 184 umol), sodium bicarbonate (927 mg, 11.0 mmol) in dioxane (10 mL) and water (3 mL) was degassed with nitrogen (5 min), and then the reaction mixture was stirred at 100° C. for 1.5 h. The mixture was cooled down to RT, diluted with ethyl acetate (20 mL) and filtered through Celite pad. The organic phase was dried over anh. Na₂SO₄, filtered, concentrated, and the crude material was triturated in 20% DCM/Hexanes to afford the title compound (620 mg, 3.10 mmol, 84% yield) as a pale brown solid, which was used in the next step without further purification.

Step 2: 4-(3-iodo-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylisoxazole

To a solution of 3-methyl-4-(1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole (500 mg, 2.50 mmol) in DMF (5 mL), was added N-iodosuccinimide (710 mg, 3.00 mmol), and the resulting mixture was stirred at RT for 3 h. The reaction mixture was then quenched with 10% aqueous sodium thiosulfate (25 mL), and the resulting suspension was stirred for 10 minutes. The suspension was then filtered to afford the title compound (757 mg, 2.32 mmol, 93% yield) as a brown solid, which was used in the next step without further purification.

Step 3: 4-(3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylisoxazole

To a solution of 4-(3-iodo-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylisoxazole (757 mg, 2.32 mmol) in DCM (10 mL), was added 3,4-dihydro-2H-pyran (240 uL, 2.55 mmol) followed by p-toluenesulfonic acid monohydrate (44.8 mg, 232 umol), and the solution was stirred at RT for 12 h. The reaction mixture was then diluted with ethyl acetate (20 mL), and the organic phase was 25 washed with aq. sat. sodium bicarbonate (2×10 mL). The organic phase was dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure to afford the title compound (952 mg, 2.32 mmol, quant. yield), which was used in the next step without further purification.

Step 4: 3-methyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole

To a mixture of 4-(3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylisoxazole (952 mg, 2.32 mmol), 4-chloro-2-(methylthio)-5-(trifluoromethyl)pyrimidine (637 mg, 2.78 mmol), and hexamethylditin (486 uL, 2.32 mmol) in toluene (13 mL), purged with nitrogen (5 min), was added Pd(PPh₃)₄ (268 mg, 232 umol), and the reaction mixture was stirred at 105° C. until full conversion (24 h). The reaction mixture was poured into a freshly prepared solution of aqueous potassium fluoride (1.0 g in 50 mL), and stirred for 30 min. The resulting mixture was filtered on Celite pad, and the filtrate was extracted with ethyl acetate (3×30 mL). The organic layers were combined, washed with brine (30 mL), dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (EtOAc in hexanes, 10 to 70% gradient) to afford the title compound (529 mg, 1.11 mmol, 48% yield).

Step 5: 3-methyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole

To a solution of 3-methyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole (500 mg, 1.05 mmol) in DCM (19 mL), was added m-CPBA (495 mg, 2.15 mmol), and the reaction mixture was stirred at RT, monitoring the conversion by LCMS. After 2.5 h with the conversion of 47%, another 0.7 eq of m-CPBA were added, and the reaction mixture was stirred at RT for 1 h. The reaction was then quenched with 10% aq. sodium thiosulfate (10 mL) and sat. aq. NaHCO₃ (10 mL). The resulting mixture was stirred for 15 minutes, then diluted with EtOAc (100 mL). The biphasic mixture was separated, and the organic phase was washed with sat. aq. NaHCO₃ (2×10 mL). The organic phase was dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure to afford the title compound (534 mg, quant. yield), which was used in the next step without further purification.

Step 6: N—((S)-6,6-dimethylpiperidin-3-yl)-4-(6-(3-methylisoxazol-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

To a solution of 3-methyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)isoxazole (534 mg, 1.05 mmol) in THF (6.4 mL), was added (S)-6,6-dimethylpiperidin-3-amine (202 mg, 1.58 mmol) followed by DIPEA (554 uL, 3.15 mmol), and the reaction mixture was stirred at RT for 1 h. The mixture was concentrated under reduced pressure, and the residue was purified by reverse phase chromatography (C18, ACN in aq. 10 mM ammonium bicarbonate buffer, pH 10, 0 to 100% gradient) to afford the title compound (143 mg, 0.26 mmol, 24% yield over two steps).

Step 7: (S)—N-(6,6-dimethylpiperidin-3-yl)-4-(6-(3-methylisoxazol-4-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine

N—((S)-6,6-dimethylpiperidin-3-yl)-4-(6-(3-methylisoxazol-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-amine (111 mg, 0.20 mmol) was dissolved in 4 N HCl in dioxane (2 mL), and the mixture was stirred at 60° C. for 2 h. The solution was then concentrated under reduced pressure, and the residue was purified by reverse phase chromatography (C18, ACN in aq. 0.1% formic acid buffer, 10 to 50% gradient) to afford the title compound (47 mg, 0.10 mmol, 50% yield) as a white HCl salt after lyophilization.

Example 60. 3-methyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole (Compound 147) Step 1: 4-(3-iodo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylisoxazole

To a solution of 3-methyl-4-(1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole [prepared from 3-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)isoxazole and 6-bromo-1H-pyrrolo[2,3-b]pyridine as in Example 59] (550 mg, 2.76 mmol) in DMF (2 mL), iodine (702 mg, 2.76 mmol) and KOH (94 mg, 5.52 mmol) were added in one portion. The reaction mixture was stirred at 75° C. for 1 h. The mixture was then cooled down to RT and quenched by addition of 10% HCl until pH was neutral, followed by the addition of aq. sat. sodium sulfite (3 mL) at 15° C. The resulting mixture was poured into water (20 mL), and the obtained solid was filtered to afford the title compound (847 mg, 2.60 mmol, 94% yield) as a pale orange solid, which was used in the next step without further purification.

Step 2: 4-(3-iodo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylisoxazole

4-(3-Iodo-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylisoxazole (847 mg, 2.60 mmol) was dissolved in THF (10 mL), and the resulting solution was cooled to 0° C. To the mixture, was added sodium tert-butoxide (325 mg, 3.38 mmol) portion wise, and the mixture was stirred for 10 min. Benzenesulfonyl chloride (332 uL, 2.60 mmol) was then added dropwise, and the reaction mixture was allowed to reach RT and stirred for 1 h. The reaction was diluted with water (60 mL), and the resulting suspension was filtered and washed with water (15 mL) to afford the title compound (1.12 g, 2.42 mmol, 93% yield) as a pale orange solid, which was used in the next step without further purification.

Step 3: 3-methyl-4-(3-(2-(methylthio)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole

To a degassed mixture of 4-(3-iodo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylisoxazole (1.28 g, 2.75 mmol) and dichlorobis(triphenylphosphine)palladium(II) (96.5 mg, 138 umol) in dioxane (25.6 mL), was added triethylamine (2.30 mL, 16.5 mmol) followed by HBP in (4,4,5,5-Tetramethyl-1,3,2-dioxaborolane; 599 uL, 4.13 mmol). The resulting yellow suspension was stirred at 80° C. in a sealed vessel for 2 h. The reaction mixture was then cooled down to RT, and 4-chloro-2-(methylthio)-5-(trifluoromethyl)pyrimidine (629 uL, 2.75 mmol) and degassed water (600 uL) were added followed by the sodium carbonate (874 mg, 8.25 mmol). The resulting mixture was stirred at 100° C. for 12 h. The mixture was then cooled down to RT, diluted with EtOAc (25 mL), filtered on Celite pad, and concentrated under reduced pressure. The crude solid was triturated with 50% MTBE in hexanes, and the suspension was filtered to afford the title compound (510 mg, 0.96 mmol, 35% yield) as a pale beige solid, which was used in the next step without further purification.

Example 61. (3S,4S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methylpiperidine-1-carboxylate (Compound 143)

To a solution of 3,5-dimethyl-4-(3-(2-(methylsulfonyl)-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)isoxazole [prepared from (3,5-dimethylisoxazol-4-yl)boronic acid and 6-bromo-1H-pyrrolo[2,3-b]pyridine, following Examples 59 and 60] (220 mg, 0.38 mmol) and racemic cis tert-butyl 3-amino-4-methylpiperidine-1-carboxylate (122 mg, 0.57 mmol) in anh. THF (3.8 mL), was added anh. DIPEA (200 uL, 1.14 mmol) at RT. The reaction mixture was stirred at 70° C. for 16 h. The mixture was diluted with EtOAc, washed with brine, dried over anh. Na₂SO₄, filtered, and concentrated under reduced pressure. The residue was purified by column silica gel chromatography (EtOAc in hexanes, 0 to 100% gradient) to provide the racemic product (137 mg, 0.19 mmol, 51% yield) as a pale yellow solid. The racemic compound was then separated by chiral HPLC using a ChiralPak IA column and 6:6:88 mixture of MeOH/DCM/Hexanes for elution. Two enantiomers were obtained: Peak 1 (tentatively assigned as (3R,4R), 36 mg) and Peak 2 (tentatively assigned as (3S,4S), 31 mg).

Example 62. (3S,4S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methylpiperidine-1-carboxylate (Compound 135) Step 1: racemic cis tert-butyl 3-((4-(6-bromo-1-(phenylsulfonyl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methylpiperidine-1-carboxylate

6-Bromo-3-(2-chloro-5-(trifluoromethyl)pyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole [prepared from 6-bromo-1H-indole and 2,4-dichloro-5-(trifluoromethyl)pyrimidine as in Example 56 and then protected as in Example 57] (360 mg, 0.70 mmol), racemic cis tert-butyl 3-amino-4-methylpiperidine-1-carboxylate (180 mg, 0.84 mmol) and DIPEA (183 uL, 1.05 mmol) were dissolved in anh. THF (7 mL). The reaction mixture was stirred at 70° C. until full conversion (4 h). The mixture was then diluted with EtOAc, washed with sat. aq. NaHCO₃, water, and brine. Organic phase was dried over anh. Na₂SO₄, filtered, and concentrated in vacuo. The residue was purified by normal phase silica gel chromatography (EtOAc in DCM, 0 to 100% gradient) to afford the title compound (473 mg, 0.68 mmol, 97% yield) as an off-white solid.

Step 2: (3S,4S)-tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methylpiperidine-1-carboxylate

Racemic cis tert-butyl 3-((4-(6-(3,5-dimethylisoxazol-4-yl)-1H-indol-3-yl)-5-(trifluoromethyl)pyrimidin-2-yl)amino)-4-methylpiperidine-1-carboxylate (292 mg, yellow solid) was separated by Chiral SFC using ChiralPak IC column, 10×250 mm 5 um, 10% MeOH, 10 mL/min, 150 bar, column T: 40° C., run time (min): 27. Two enantiomers were obtained: Peak 1 (tentatively assigned as (3S,4S), 43 mg, white solid, ee=99.7%) and Peak 2 (tentatively assigned as (3R,4R), 38 mg, white solid, ee=99.15%).

The table of FIG. 3 provides additional details of the synthesis of certain compounds of the invention, as well as their NMR (nuclear magnetic resonance) and MS (mass spectroscopy) values.

Example 63. Inhibition of CDK Kinase Activity

Compounds described herein were assayed for inhibition of CDK7, CDK9, CDK12, and CDK2 activity at Biortus Biosciences (Jiangyin, Jiangsu Province, P.R. of China) using kinase assays for each CDK developed with a Caliper/LabChip EZ Reader (Perkin Elmer, Waltham, Mass.). These assays measure the amount of phosphorylated peptide substrate produced as a fraction of the total peptide following an incubation period at 27° C. with the following components: test compounds (variable concentrations from 10 μM down to 0.508 nM in a series of 3-fold serial dilutions), active CDK kinase protein (with the indicated cyclin, listed below for each CDK), ATP (2 mM), and substrate peptide (listed below) in the buffer 2-(N-morpholino)ethanesulfonate (MES buffer, 20 mM), pH 6.75, 0.01% (v/v) Tween 20 detergent, 0.05 mg/mL bovine serum albumin (BSA).

Specifically, the CDK7 inhibition assay used CDK7/Cyclin H/MAT1 complex (6 nM) and “5-FAM-CDK7tide” peptide substrate (2 μM, synthesized fluorophore-labeled peptide with the following sequence: 5-FAM-YSPTSPSYSPTSPSYSPTSPSKKKK (SEQ ID NO:1), where “5-FAM” means 5-carboxyfluorescein) with 6 mM MgCl₂ in the buffer composition listed above. Furthermore, the CDK9 inhibition assay used CDK9/Cyclin T1 complex (8 nM) and “5-FAM-CDK9tide” peptide substrate (2 μM, synthesized fluorophore-labeled peptide with the following sequence: 5-FAM-GSRTPMY-NH₂ (SEQ ID NO:2) where 5-FAM is defined above and NH₂ signifies a C-terminal amide) with 10 mM MgCl₂ in the buffer composition listed above. The CDK12 inhibition assay used CDK12 (aa686-1082)/Cyclin K complex (50 nM) and “5-FAM-CDK9tide” (2 μM) as defined above, with 2 mM MgCl₂ in the buffer composition above. Additionally, the CDK2 inhibition assay used CDK2/Cyclin E1 complex (0.5 nM) and “5-FAM-CDK7tide” (2 μM; defined above) with 2 mM MgCl₂ in the buffer composition above.

The incubation period at 27° C. for each CDK inhibition assay was chosen such that the fraction of phosphorylated peptide product produced in each assay, relative to the total peptide concentration, was approximately 20% (±5%) for the uninhibited kinase (35 min. for CDK7, 35 min. for CDK2, 3 hr. for CDK12, 15 min. for CDK9). In cases where the compound titrations were tested and resulted in inhibition of peptide product formation, these data were fit to produce best-fit IC₅₀ values. The results of these assays are shown below in Table 1 where “A” represents a calculated IC₅₀ of less than 30 nM; “B” represents a calculated IC₅₀ of between 30 nM and less than 100 nM; “C” represents a calculated IC₅₀ of between 100 nM and less than 500 nM; “D” represents a calculated IC₅₀ of greater than or equal to 500 nM, and “NT” represents that the specified compound was not tested in the specified assay.

The inhibitory activity of selected compounds against CDK2, CDK7, CDK9, and CDK12 was found to be as follows:

CDK CDK CDK CDK Compound 12 2 7 9 100 D D A D 101 C D A D 102 D D A D 103 C D A D 104 D D A D 105 D D A D 106 D D A D 107 D D A D 108 D D A D 109 D D A D 110 D D A D 111 D D A D 112 D D A D 113 D D A D 114 D D A D 115 C C A D 116 D D A D 117 D D A D 118 D D A D 119 D D A D 120 D D A D 121 D D A D 122 D D A D 123 D D A D 124 D D A D 125 D D A D 126 D D A D 127 D D A D 128 D D A D 129 D D A D 130 D D A D 131 D D A D 132 D D A D 133 D D A D 134 D D A D 135 D D B D 136 D D A D 137 D D A D 138 D D A D 139 D D A D 140 D D A D 141 D D A D 142 D D A D 143 D D A D 144 D D A D 145 D D A D 146 D D A D 147 D D A D 148 D D A D 149 D D A D 150 D D A D 151 D D A D 152 D D A D 153 D D A D 154 D D A D 155 D D A D 156 D D A D 157 D D A D 158 D D A D 159 D D A D 160 D D A D 161 D D A D 162 D D A D 163 D D A D 164 D D A D 165 D D B D 166 D D A D 167 D D A D 168 D D A D

Example 64. Inhibition of Cell Proliferation

HCC70 and MB453 cells are cell lines derived from human triple negative breast cancer. COV318 and COV504 cells are cell lines derived from human ovarian cancer. Representative compounds of the invention were tested at different concentrations (from 4 μM to 126.4 μM; 0.5 log serial dilutions) for their ability to inhibit the proliferation of each of these cell lines. Known CDK inhibitors dinaciclib or N-((1S,3R)-3-((5-chloro-4-(1H-indol-3-yl) pyrimidin-2-yl)amino)cyclohexyl)-5-((E)-4-(dimethylamino)but-2-enamido)picolinamide and triptolide were used as positive controls. Cells were seeded at approximately 2,000 cells/well and grown in ATCC-formulated RPMI-1640 Medium (ATCC 30-2001)+10% FBS. The cells were cultured at 37° C. in a humidified chamber in the presence of 5% CO₂. Proliferation assays were conducted over a 72-hour time period. CyQUANT® Direct Cell Proliferation Assay (Life Technologies, Chicago, Ill. USA) was used to assess the anti-proliferative effects of the compounds following manufacturer's directions and utilizing the reagents supplied with the CyQUANT® Direct Cell kit. The results of the assay are shown below in Table 2 where “A” represents a calculated IC₅₀ of less than 100 nM; “B” represents a calculated IC₅₀ of between 100 nM and less than 500 nM; “C” represents a calculated IC₅₀ of between 500 nM and less than 1 μM; “D” represents a calculated IC₅₀ of greater than 1 μM. Cell proliferation inhibition activity of selected compounds against HCC70, MB453, COV318 and COV504 cells was found to be as follows:

Compound HCC70 COV318 COV504 MB453 100 A B A A 101 A A A A 102 A B A A 103 B B A A 104 A B A A 105 A C B B 106 A B A A 107 B B B B 108 A A A A 109 B A A B 110 A B A A 111 B B A B 112 B D B B 113 C D C B 114 A A A A 115 A A A A 116 A A A A 117 B C A A 118 A B A A 119 A D A A 120 B C B A 121 B B A A 122 B D A A 123 B B A A 124 A A A A 125 B B A A 126 A B A A 127 D B A A 128 A B A A 129 A A A A 130 B B B B 131 B B A A 132 A A A A 133 A B A A 134 A A A A 135 B D A A 136 A D A A 137 A A A A 138 A A A A 139 A D A A 140 D D B C 141 B B A B 142 A C A A 143 A D A A 144 A D A A 145 B D B B 146 C D B B 147 A D A A 148 D D C B 149 A A A A 150 B B A A 151 D D D C 152 D D C B 153 A A A A 154 B D B D 155 A A A A 156 C D B B 157 A A A A 158 A B A A 159 A D A A 160 D D B B 161 A B A A 162 B D A C 163 A D A A 164 B C A A 165 D D C C 166 A A A A 167 A B A B 168 A A A A

In the claims, articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context (for example, where it is evident from the context that “A or B” can mean only “A” or, alternatively, only “B”). The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process as well as embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.

Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims are introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists every possible subgroup of the elements is also disclosed, and any element(s) can be removed from the group. In general, where the invention, or aspects or embodiments of the invention, is/are referred to as comprising or including particular elements and/or features, other aspects or embodiments of the invention consist of, or consist essentially of, such elements and/or features. For practicality and simplicity, not all of those aspects or embodiments have been specifically set forth in haec verba herein but are nevertheless within the scope of the present invention. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, and any value may be as stated or “about” the stated value.

One of ordinary skill in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the compositions and methods described and claimed herein. Such equivalents are intended to be encompassed by the following claims. 

1. A pharmaceutical composition, wherein the composition is formulated for oral administration and comprises a pharmaceutically acceptable excipient and a compound of Formula (I):

or a pharmaceutically acceptable salt, stereoisomer, or isotopic form thereof, wherein: ring A is

ring B is

wherein each of R², R³, R⁴ and R⁵ are, independently, hydrogen or —CH₃; X and Y are, independently, N or CH; R¹ is hydrogen or fluoro; and the compound is other than:


2. The pharmaceutical composition of claim 1, wherein ring A is

3.-4. (canceled)
 5. The pharmaceutical composition of claim 1, wherein ring B is

6.-7. (canceled)
 8. The pharmaceutical composition of claim 1, wherein ring A is

and ring B is


9. The pharmaceutical composition of claim 1, wherein X is CH and Y is CH.
 10. The pharmaceutical composition of claim 1, wherein X is N.
 11. A pharmaceutical composition, wherein the composition is formulated for oral administration and comprises a pharmaceutically acceptable excipient and a compound of Formula II:

or a pharmaceutically acceptable salt, stereoisomer, or isotopic form thereof, wherein: ring A is

and R¹ is hydrogen or fluoro.
 12. The pharmaceutical composition of claim 1, wherein the compound of Formula (I) is selected from the group consisting of:

or a pharmaceutically acceptable salt, stereoisomer, or isotopic form thereof.
 13. A pharmaceutical composition, wherein the composition is formulated for oral administration and comprises a pharmaceutically acceptable excipient and a compound selected from the group consisting of:

or a pharmaceutically acceptable salt, stereoisomer, or isotopic form thereof.
 14. (canceled)
 15. A method of treating a patient suffering from a disease associated with aberrant activity of CDK7, wherein the disease is a proliferative disease, an infectious disease, or a disease caused by or associated with expanded repeats of simple nucleotide tracts, and the method comprises a step of administering to the patient a therapeutically effective amount of the pharmaceutical composition of claim
 1. 16.-17. (canceled)
 18. The method of claim 15, wherein the proliferative disease is a cancer or benign neoplasm.
 19. The method of claim 18, wherein the cancer is a blood cancer, a bone cancer, a brain cancer, a breast cancer, a colorectal cancer, a lung cancer, a melanoma, a neuroblastoma, an ovarian cancer, or a pancreatic cancer.
 20. The method of claim 19, wherein the blood cancer is chronic lymphocytic leukemia (CLL), chronic myelomonocytic leukemia (CMML), acute lymphoblastic leukemia (ALL), T-cell acute lymphoblastic leukemia (T-ALL), chronic myelogenous leukemia (CML), lymphoma, or multiple myeloma. 21.-25. (canceled)
 26. The method of claim 19, wherein the blood cancer is acute myelogenous leukemia (AML).
 27. The method of claim 19, wherein the bone cancer is osteosarcoma or Ewing's sarcoma.
 28. The method of claim 19, wherein the breast cancer is triple-negative breast cancer (TNBC).
 29. The method of claim 19, wherein the cancer is a brain cancer.
 30. The method of claim 19, wherein the lung cancer is small cell lung cancer (SCLC).
 31. The method of claim 19, wherein the cancer is a colorectal cancer, a melanoma, a neuroblastoma, an ovarian cancer, or a pancreatic cancer.
 32. The method of claim 15, wherein the method further comprises a step of administering, to the patient, a therapeutically effective amount of an anti-proliferative agent, an anti-cancer agent, an immunosuppressant agent, or a pain-relieving agent. 